diff --git a/01_runBasecall.sh b/01_runBasecall.sh
index 9dd7f1b..5bccb44 100644
--- a/01_runBasecall.sh
+++ b/01_runBasecall.sh
@@ -2,8 +2,8 @@
 
 ## Allocate resources
 #SBATCH --time=3-00:00:00
-#SBATCH --mem-per-cpu=8G
-#SBATCH --cpus-per-task=8
+#SBATCH --mem-per-cpu=16G
+#SBATCH --cpus-per-task=4
 
 ## job name
 #SBATCH --job-name="guppy"
diff --git a/02_runAlignFastq.sh b/02_runAlignFastq.sh
index 7fb2bd8..aaf9854 100644
--- a/02_runAlignFastq.sh
+++ b/02_runAlignFastq.sh
@@ -3,7 +3,9 @@
 ## Allocate resources
 #SBATCH --time=2-00:00:00
 #SBATCH --mem-per-cpu=8G
-#SBATCH --array=4
+#SBATCH --array=1-6
+#SBATCH --mail-user=jennifer.semple@izb.unibe.ch
+#SBATCH --mail-type=END,FAIL
 ## you should submit as many jobs as there are barcodes in barcodesOfInterest
 ## (don't forget to include unclassfied in barcodesOfInterst in the varSettings.sh file)
 
diff --git a/02_runAlignFastqdb.sh b/02_runAlignFastqdb.sh
new file mode 100644
index 0000000..bac581a
--- /dev/null
+++ b/02_runAlignFastqdb.sh
@@ -0,0 +1,33 @@
+#! /bin/bash
+
+## Allocate resources
+#SBATCH --time=2-00:00:00
+#SBATCH --mem-per-cpu=8G
+#SBATCH --array=1-6
+#SBATCH --mail-user=jennifer.semple@izb.unibe.ch
+#SBATCH --mail-type=END,FAIL
+## you should submit as many jobs as there are barcodes in barcodesOfInterest
+## (don't forget to include unclassfied in barcodesOfInterst in the varSettings.sh file)
+
+## job name
+#SBATCH --job-name="npAlign"
+
+# read in the run specific settings
+source ./varSettings.sh
+
+
+let i=$SLURM_ARRAY_TASK_ID-1
+
+# organise fastq, do QC plots and align with minimap
+./alignFastqdb.sh ${expName} ${barcodesOfInterest[$i]} ${genomeFile}
+
+
+# if barcode is one with a spikein, align also to other genomes
+for bc in ${bcWithSpikeIn[@]}
+do
+    if [ "${barcodesOfInterest[$i]}" == "$bc" ]; then
+        ./alignFastqdb_spikeIn.sh ${expName} ${barcodesOfInterest[$i]} ${lambdaFile}
+        ./alignFastqdb_spikeIn.sh ${expName} ${barcodesOfInterest[$i]} ${phiXfile}
+    	exit
+    fi
+done
diff --git a/alignFastq.sh b/alignFastq.sh
index 8abc5cd..15e58de 100755
--- a/alignFastq.sh
+++ b/alignFastq.sh
@@ -2,16 +2,14 @@
 ## script to arrange all fastq files into batches for analysis. Combined files will be created for
 ## each barcode of interest for both passed and failed reads (e.g. pass_barcode01 or fail_barcode01).  
 
+source ./varSettings.sh
 # Get variables from command line
 expName=$1 	# experiment name (date of exp usually)
 bc=$2 		# barcode
 genomeFile=$3 	# full path to reference genome
 
 # need absolute paths for nanopolish index. get it from the summary file.
-#summaryFile=`readlink -f ../fastqFiles/sequencing_summary.txt`
-expPath=`readlink -f ../`
-#expPath=/data/projects/p025/Jenny/20190411_dSMFv021-025np_N2gw
-summaryFile=${expPath}/fastqFiles/sequencing_summary.txt
+summaryFile=${workDir}/fastqFiles/sequencing_summary.txt
 
 ####### modules to load ##########
 module load vital-it
@@ -21,78 +19,61 @@ module add UHTS/Analysis/samtools/1.8;
 ############################################
 
 
-##########################################################
-# function to run Pauvre and nanoQC on individual batches
-##########################################################
-
-## activate python environment for QC programmes (Pauvre and NanoQC)
-source activate albacore_env
-
-## function for running Pauvre and NanoQC on each combined file
-do_pauvre_nanoQC() {
-   # get variables from arguments
-   bc=$1 #barcode
-   pf=$2 #pass or fail folder
-   eN=$3 #expName
-   qc=$4 #qcDir
-   fq=${expPath}/bcFastq/${eN}_${pf}_${bc}.fastq.gz #input file to qc
-   
-   # assemble names for some of the output files
-   outDir=${qc}/${pf}_${bc}
-   mkdir -p $outDir
-   outStats=${outDir}/pauvreStats.txt
-   
-   # run QC programmes
-   pauvre stats -f $fq > ${outStats}
-   nanoQC $fq -o $outDir
-}
-
-
-################################################
-# Collecting reads from barcodes that were used
-################################################
-echo "collecting reads from folder of barcodes that were used..."
-
-# merge all reads from particular barcode into single file (pass fail separately)
-echo ${expPath}/fast5Files
-
-if [ -d ${expPath}/bcFastq/pass/${bc} ];
-then
-    echo "passed reads..."
-    cat ${expPath}/bcFastq/pass/${bc}/*.fastq > ${expPath}/bcFastq/${expName}_pass_${bc}.fastq
-    gzip ${expPath}/bcFastq/${expName}_pass_${bc}.fastq
-    rm ${expPath}/bcFastq/${expName}_pass_${bc}.fastq
-    ${NANOPOLISH_DIR}/nanopolish index -s ${summaryFile} -d ${expPath}/fast5Files ${expPath}/bcFastq/${expName}_pass_${bc}.fastq.gz
-    do_pauvre_nanoQC $bc pass $expName ${expPath}/qc
-fi
-
-    if [ -d ${expPath}/bcFastq/fail/${bc} ];
-then
-    echo "failed reads ..."
-    cat ${expPath}/bcFastq/fail/${bc}/*.fastq > ${expPath}/bcFastq/${expName}_fail_${bc}.fastq
-    gzip ${expPath}/bcFastq/${expName}_fail_${bc}.fastq
-    rm ${expPath}/bcFastq/${expName}_fail_${bc}.fastq
-    ${NANOPOLISH_DIR}/nanopolish index -s ${summaryFile} -d ${expPath}/fast5Files ${expPath}/bcFastq/${expName}_fail_${bc}.fastq.gz
-    do_pauvre_nanoQC $bc fail $expName ${expPath}/qc
-fi
-
-
-################################################
-# aligning to genome
-################################################
-
-echo "aligning to genome..."
-
-mkdir -p ${expPath}/bamFiles
-
- #map reads to genome with minimap2
-# filter reads with flag=2308: unmapped (4) + secondary alignment (256) + supplementary alignment (2048) [the latter category is the main problem]
-minimap2 -ax map-ont $genomeFile ${expPath}/bcFastq/${expName}_pass_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T ${expName}_pass_${bc}  -o ${expPath}/bamFiles/${expName}_pass_${bc}.sorted.bam 
-minimap2 -ax map-ont $genomeFile ${expPath}/bcFastq/${expName}_fail_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T ${expName}_fail_${bc} -o ${expPath}/bamFiles/${expName}_fail_${bc}.sorted.bam
-
-echo "index bam file ..."
-samtools index ${expPath}/bamFiles/${expName}_pass_${bc}.sorted.bam
-samtools index ${expPath}/bamFiles/${expName}_fail_${bc}.sorted.bam
+source ${HOME}/.bashrc
+source ${CONDA_ACTIVATE} nanopore
+
+
+#################################################
+## Collecting reads from barcodes that were used
+#################################################
+#echo "collecting reads from folder of barcodes that were used..."
+#
+## merge all reads from particular barcode into single file (pass fail separately)
+#echo ${dataDir}/fast5Files
+#mkdir -p ${workDir}/qc/NanoStat
+#
+#if [ -d "${workDir}/bcFastq/pass/${bc}" ];
+#then
+#    echo "passed reads..."
+#    cat ${workDir}/bcFastq/pass/${bc}/*.fastq > ${workDir}/bcFastq/${expName}_pass_${bc}.fastq
+#    gzip ${workDir}/bcFastq/${expName}_pass_${bc}.fastq
+#    rm ${workDir}/bcFastq/${expName}_pass_${bc}.fastq
+#    nanopolish index -s ${summaryFile} -d ${dataDir}/fast5Files ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz
+#    mkdir -p ${workDir}/qc/pass_${bc}
+#    nanoQC ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz -o ${workDir}/qc/pass_${bc}
+#    NanoStat --fastq ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz  --outdir ${workDir}/qc/NanoStat --name NanoStat_${expName}_pass_${bc}.txt --readtype 1D 
+#fi
+#
+#if [ -d "${workDir}/bcFastq/fail/${bc}" ];
+#then
+#    echo "failed reads ..."
+#    cat ${workDir}/bcFastq/fail/${bc}/*.fastq > ${workDir}/bcFastq/${expName}_fail_${bc}.fastq
+#    gzip ${workDir}/bcFastq/${expName}_fail_${bc}.fastq
+#    rm ${workDir}/bcFastq/${expName}_fail_${bc}.fastq
+#    nanopolish index -s ${summaryFile} -d ${dataDir}/fast5Files ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz
+#    mkdir -p ${workDir}/qc/fail_${bc}
+#    nanoQC ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz -o ${workDir}/qc/fail_${bc}
+#    NanoStat --fastq ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz  --outdir ${workDir}/qc/NanoStat --name NanoStat_${expName}_fail_${bc}.txt --readtype 1D
+#fi
+#
+#
+#################################################
+## aligning to genome
+#################################################
+#
+#echo "aligning to genome..."
+#
+#mkdir -p ${workDir}/bamFiles
+#
+## map reads to genome with minimap2
+## filter reads with flag=2308: unmapped (4) + secondary alignment (256) + supplementary alignment (2048) [the latter category is the main problem]
+#minimap2 -ax map-ont $genomeFile ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T pass_${bc}  -o ${workDir}/bamFiles/${expName}_pass_${bc}.sorted.bam 
+#minimap2 -ax map-ont $genomeFile ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T fail_${bc} -o ${workDir}/bamFiles/${expName}_fail_${bc}.sorted.bam
+#
+#echo "index bam file ..."
+#samtools index ${workDir}/bamFiles/${expName}_pass_${bc}.sorted.bam
+#samtools index ${workDir}/bamFiles/${expName}_fail_${bc}.sorted.bam
+#
 
 
 ################################################
@@ -111,76 +92,101 @@ chr=( `cut -f1 chrom.sizes` )
 # identifying CmG
 ################################################
 echo "identify CmG ..."
+doFail=FALSE
 
-mkdir -p ${expPath}/meth_calls/
+mkdir -p ${workDir}/meth_calls/
 
 for i in "${!chr[@]}"
 do
-	${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${expPath}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${expPath}/bamFiles/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${expPath}/meth_calls/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv
-
-	${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${expPath}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${expPath}/bamFiles/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${expPath}/meth_calls/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv
+	nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${workDir}/bamFiles/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_calls/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv
+  if [ "$doFail" = "TRUE" ]
+  then
+	echo "analysing failed reads"
+	nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${workDir}/bamFiles/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_calls/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv
+  fi
 done
 
 
 #### combine separate chromosomes into single file ####
 
 # first write header
-head -1 ${expPath}/meth_calls/${expName}_pass_${bc}_CpGcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${expName}_pass_${bc}_CpGcalls.tsv
-head -1 ${expPath}/meth_calls/${expName}_fail_${bc}_CpGcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${expName}_fail_${bc}_CpGcalls.tsv
+head -1 ${workDir}/meth_calls/${expName}_pass_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${expName}_pass_${bc}_CpGcalls.tsv
+if [ "$doFail" = TRUE ]
+then
+  head -1 ${workDir}/meth_calls/${expName}_fail_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${expName}_fail_${bc}_CpGcalls.tsv
+fi
+
 
 # then combine files
 for i in "${!chr[@]}"
 do
-        tail -n +2 ${expPath}/meth_calls/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${expName}_pass_${bc}_CpGcalls.tsv
-        tail -n +2 ${expPath}/meth_calls/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${expName}_fail_${bc}_CpGcalls.tsv
-        rm ${expPath}/meth_calls/${expName}_????_${bc}_CpGcalls_${chr[$i]}.tsv
+        tail -n +2 ${workDir}/meth_calls/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${expName}_pass_${bc}_CpGcalls.tsv
+  if [ "$doFail" = TRUE ]
+  then
+        tail -n +2 ${workDir}/meth_calls/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${expName}_fail_${bc}_CpGcalls.tsv
+  fi
+        rm ${workDir}/meth_calls/${expName}_????_${bc}_CpGcalls_${chr[$i]}.tsv
 done
 
 
 #### caclulating frequency ######
-mkdir -p ${expPath}/meth_freq
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${expName}_pass_${bc}_CpGcalls.tsv > ${expPath}/meth_freq/${expName}_pass_${bc}_freqCmG.tsv
-
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${expName}_fail_${bc}_CpGcalls.tsv > ${expPath}/meth_freq/${expName}_fail_${bc}_freqCmG.tsv
+mkdir -p ${workDir}/meth_freq
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${expName}_pass_${bc}_CpGcalls.tsv > ${workDir}/meth_freq/${expName}_pass_${bc}_freqCmG.tsv
 
+if [ "$doFail" = TRUE ]
+then
+	${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${expName}_fail_${bc}_CpGcalls.tsv > ${workDir}/meth_freq/${expName}_fail_${bc}_freqCmG.tsv
+fi
 
 ################################################
 # identifying GCm
 ################################################
 echo "identify GCm ..."
 
-mkdir -p ${expPath}/meth_calls/
+mkdir -p ${workDir}/meth_calls/
 
 for i in "${!chr[@]}"
 do
-echo ${chr[$i]}
-echo ${chrIntervals[$i]}
-	${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -r ${expPath}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${expPath}/bamFiles/${expName}_pass_${bc}.sorted.bam -g $genomeFile -w ${chrIntervals[$i]} > ${expPath}/meth_calls/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv
-
-	${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -r ${expPath}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${expPath}/bamFiles/${expName}_fail_${bc}.sorted.bam -g $genomeFile -w ${chrIntervals[$i]} > ${expPath}/meth_calls/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv
+	echo ${chr[$i]}
+	echo ${chrIntervals[$i]}
+	nanopolish call-methylation -t 4 -q gpc -r ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${workDir}/bamFiles/${expName}_pass_${bc}.sorted.bam -g $genomeFile -w ${chrIntervals[$i]} > ${workDir}/meth_calls/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv
+
+  	if [ "${doFail}" = TRUE ]
+  	then
+		nanopolish call-methylation -t 4 -q gpc -r ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${workDir}/bamFiles/${expName}_fail_${bc}.sorted.bam -g $genomeFile -w ${chrIntervals[$i]} > ${workDir}/meth_calls/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv
+	fi
 done
 
 
 #### combine separate chromosomes into single file ####
 
 # first write header
-head -1 ${expPath}/meth_calls/${expName}_pass_${bc}_GpCcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${expName}_pass_${bc}_GpCcalls.tsv
-head -1 ${expPath}/meth_calls/${expName}_fail_${bc}_GpCcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${expName}_fail_${bc}_GpCcalls.tsv 
+head -1 ${workDir}/meth_calls/${expName}_pass_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${expName}_pass_${bc}_GpCcalls.tsv
+if [ "$doFail" = TRUE ]
+then
+	head -1 ${workDir}/meth_calls/${expName}_fail_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${expName}_fail_${bc}_GpCcalls.tsv 
+fi
 
 # then combine files
 for i in "${!chr[@]}"
 do 
-	tail -n +2 ${expPath}/meth_calls/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${expName}_pass_${bc}_GpCcalls.tsv
-	tail -n +2 ${expPath}/meth_calls/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${expName}_fail_${bc}_GpCcalls.tsv
-	rm ${expPath}/meth_calls/${expName}_????_${bc}_GpCcalls_${chr[$i]}.tsv
+	tail -n +2 ${workDir}/meth_calls/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${expName}_pass_${bc}_GpCcalls.tsv
+  	if [ "$doFail" = TRUE ]
+  	then
+		tail -n +2 ${workDir}/meth_calls/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${expName}_fail_${bc}_GpCcalls.tsv
+	fi
+	rm ${workDir}/meth_calls/${expName}_????_${bc}_GpCcalls_${chr[$i]}.tsv
 done
 
 
 #### caclulating frequency ######
-mkdir -p ${expPath}/meth_freq
+mkdir -p ${workDir}/meth_freq
 
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${expName}_pass_${bc}_GpCcalls.tsv > ${expPath}/meth_freq/${expName}_pass_${bc}_freqGCm.tsv
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${expName}_pass_${bc}_GpCcalls.tsv > ${workDir}/meth_freq/${expName}_pass_${bc}_freqGCm.tsv
 
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${expName}_fail_${bc}_GpCcalls.tsv > ${expPath}/meth_freq/${expName}_fail_${bc}_freqGCm.tsv
+if [ "$doFail" = TRUE ]
+then
+	${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${expName}_fail_${bc}_GpCcalls.tsv > ${workDir}/meth_freq/${expName}_fail_${bc}_freqGCm.tsv
+fi
 
 
diff --git a/alignFastq_spikeIn.sh b/alignFastq_spikeIn.sh
index a86a09d..a393560 100755
--- a/alignFastq_spikeIn.sh
+++ b/alignFastq_spikeIn.sh
@@ -9,10 +9,6 @@ genomeFile=$3 	# full path to reference genome
 genomeName=`basename $genomeFile`
 genomeName=${genomeName%.fasta}
 
-# need absolute paths for nanopolish index. get it from the summary file.
-#summaryFile=`readlink -f ../fastqFiles/sequencing_summary.txt`
-#expPath=`dirname $summaryFile`
-expPath=`readlink -f ../`
 
 ####### modules to load ##########
 module load vital-it
@@ -24,22 +20,24 @@ module add UHTS/Analysis/samtools/1.8;
 
 
 
-################################################
-# aligning to genome
-################################################
-
-echo "aligning to genome..."
-
-mkdir -p ../bamFiles/${genomeName}
 
-# map reads to genome with minimap2
-# filter reads with flag=2308: unmapped (4) + secondary alignment (256) + supplementary alignment (2048) [the latter category is the main problem]
-minimap2 -ax map-ont $genomeFile ../bcFastq/${expName}_pass_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T ${genomeName}_${expName}_pass_${bc} -o ../bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam 
-minimap2 -ax map-ont $genomeFile ../bcFastq/${expName}_fail_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T ${genomeName}_${expName}_pass_${bc} -o ../bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam
+#################################################
+## aligning to genome
+#################################################
+#
+#echo "aligning to genome..."
+#
+#mkdir -p ../bamFiles/${genomeName}
+#
+## map reads to genome with minimap2
+## filter reads with flag=2308: unmapped (4) + secondary alignment (256) + supplementary alignment (2048) [the latter category is the main problem]
+#minimap2 -ax map-ont $genomeFile ../bcFastq/${expName}_pass_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T tmp -o ../bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam 
+#minimap2 -ax map-ont $genomeFile ../bcFastq/${expName}_fail_${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T tmp -o ../bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam
+#
+#echo "index bam file ..."
+#samtools index ../bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam
+#samtools index ../bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam
 
-echo "index bam file ..."
-samtools index ../bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam
-samtools index ../bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam
 
 
 ################################################
@@ -63,32 +61,32 @@ echo "identify CmG ..."
 mkdir -p ../meth_calls/${genomeName}
 for i in "${!chr[@]}"
 do
-${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${expPath}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${expPath}/bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv
+${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${workDir}/bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv
 
-${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${expPath}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${expPath}/bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv
+#${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${workDir}/bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv
 done
 
 
 #### combine separate chromosomes into single file ####
 
 # first write header
-head -1 ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv
-head -1 ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv
+head -1 ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv
+#head -1 ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv
 
 # then combine files
 for i in "${!chr[@]}"
 do
-        tail -n +2 ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv
-        tail -n +2 ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv
-        rm ${expPath}/meth_calls/${genomeName}/${expName}_????_${bc}_CpGcalls_${chr[$i]}.tsv
+        tail -n +2 ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv
+#       tail -n +2 ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv
+        rm ${workDir}/meth_calls/${genomeName}/${expName}_????_${bc}_CpGcalls_${chr[$i]}.tsv
 done
 
 
 #### caclulating frequency ######
 mkdir -p ../meth_freq/${genomeName}
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv > ${expPath}/meth_freq/${genomeName}/${expName}_pass_${bc}_freqCmG.tsv
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv > ${workDir}/meth_freq/${genomeName}/${expName}_pass_${bc}_freqCmG.tsv
 
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv > ${expPath}/meth_freq/${genomeName}/${expName}_fail_${bc}_freqCmG.tsv
+#${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv > ${workDir}/meth_freq/${genomeName}/${expName}_fail_${bc}_freqCmG.tsv
 
 
 
@@ -100,30 +98,30 @@ echo "identify GCm ..."
 mkdir -p ../meth_calls/${genomeName}
 for i in "${!chr[@]}"
 do
-${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -w ${chrIntervals[$i]} -r ${expPath}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${expPath}/bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv
+${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -w ${chrIntervals[$i]} -r ${workDir}/bcFastq/${expName}_pass_${bc}.fastq.gz -b ${workDir}/bamFiles/${genomeName}/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv
 
-${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -w ${chrIntervals[$i]} -r ${expPath}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${expPath}/bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv
+#${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -w ${chrIntervals[$i]} -r ${workDir}/bcFastq/${expName}_fail_${bc}.fastq.gz -b ${workDir}/bamFiles/${genomeName}/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv
 done
 
 
 #### combine separate chromosomes into single file ####
 
 # first write header
-head -1 ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv
-head -1 ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[0]}.tsv > ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv 
+head -1 ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv
+#head -1 ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv 
 
 # then combine files
 for i in "${!chr[@]}"
 do 
-    tail -n +2 ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv
-    tail -n +2 ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv >> ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv
-    rm ${expPath}/meth_calls/${genomeName}/${expName}_????_${bc}_GpCcalls_${chr[$i]}.tsv
+    tail -n +2 ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv
+#    tail -n +2 ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv
+    rm ${workDir}/meth_calls/${genomeName}/${expName}_????_${bc}_GpCcalls_${chr[$i]}.tsv
 done
 
 
 
 #### caclulating frequency ######
 mkdir -p ../meth_freq/${genomeName}
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv > ${expPath}/meth_freq/${genomeName}/${expName}_pass_${bc}_freqGCm.tsv
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv > ${workDir}/meth_freq/${genomeName}/${expName}_pass_${bc}_freqGCm.tsv
 
-${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${expPath}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv > ${expPath}/meth_freq/${genomeName}/${expName}_fail_${bc}_freqGCm.tsv
+#${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_calls/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv > ${workDir}/meth_freq/${genomeName}/${expName}_fail_${bc}_freqGCm.tsv
diff --git a/alignFastqdb.sh b/alignFastqdb.sh
new file mode 100644
index 0000000..1ece788
--- /dev/null
+++ b/alignFastqdb.sh
@@ -0,0 +1,183 @@
+#! /bin/bash
+## script to arrange all fastq files into batches for analysis. Combined files will be created for
+## each barcode of interest for both passed and failed reads (e.g. pass_barcode01 or fail_barcode01).  
+
+source ./varSettings.sh
+# Get variables from command line
+expName=$1 	# experiment name (date of exp usually)
+bc=$2 		# barcode
+genomeFile=$3 	# full path to reference genome
+
+# need absolute paths for nanopolish index. get it from the summary file.
+summaryFile=${workDir}/fastqFiles/sequencing_summary.txt
+
+####### modules to load ##########
+module load vital-it
+#module load R/3.5.1
+module add UHTS/Analysis/minimap2/2.12;
+module add UHTS/Analysis/samtools/1.8;
+############################################
+
+source ${HOME}/.bashrc
+source ${CONDA_ACTIVATE} nanopore
+
+
+#################################################
+## Collecting reads from barcodes that were used
+#################################################
+#echo "collecting reads from folder of barcodes that were used..."
+#
+## merge all reads from particular barcode into single file (pass fail separately)
+#echo ${dataDir}/fast5Files
+#mkdir -p ${workDir}/qc/NanoStatdb
+#
+#if [ -f ${workDir}/dbbcFastq/pass/${bc}.fastq.gz ];
+#then
+#    echo "passed reads..."
+#    nanopolish index -s ${summaryFile} -d ${dataDir}/fast5Files ${workDir}/dbbcFastq/pass/${bc}.fastq.gz
+#    mkdir -p ${workDir}/qc/db_pass_${bc}
+#    nanoQC ${workDir}/dbbcFastq/pass/${bc}.fastq.gz -o ${workDir}/qc/db_pass_${bc}
+#    NanoStat --fastq ${workDir}/dbbcFastq/pass/${bc}.fastq.gz  --outdir ${workDir}/qc/NanoStatdb --name NanoStat_${expName}_pass_${bc}.txt --readtype 1D 
+#fi
+#
+#if [ -f ${workDir}/dbbcFastq/fail/${bc}.fastq.gz ];
+#then
+#    echo "failed reads ..."
+#    nanopolish index -s ${summaryFile} -d ${dataDir}/fast5Files ${workDir}/dbbcFastq/fail/${bc}.fastq.gz
+#    mkdir -p ${workDir}/qc/db_fail_${bc}
+#    nanoQC ${workDir}/dbbcFastq/fail/${bc}.fastq.gz -o ${workDir}/qc/db_fail_${bc}
+#    NanoStat --fastq ${workDir}/dbbcFastq/fail/${bc}.fastq.gz  --outdir ${workDir}/qc/NanoStatdb --name NanoStat_${expName}_fail_${bc}.txt --readtype 1D
+#fi
+#
+#
+#################################################
+## aligning to genome
+#################################################
+#
+#echo "aligning to genome..."
+#
+#mkdir -p ${workDir}/bamFilesdb
+#
+## map reads to genome with minimap2
+## filter reads with flag=2308: unmapped (4) + secondary alignment (256) + supplementary alignment (2048) [the latter category is the main problem]
+#minimap2 -ax map-ont $genomeFile ${workDir}/dbbcFastq/pass/${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T pass_${bc} -o ${workDir}/bamFilesdb/${expName}_pass_${bc}.sorted.bam 
+#minimap2 -ax map-ont $genomeFile ${workDir}/dbbcFastq/fail/${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T fail_${bc} -o ${workDir}/bamFilesdb/${expName}_fail_${bc}.sorted.bam
+#
+#echo "index bam file ..."
+#samtools index ${workDir}/bamFilesdb/${expName}_pass_${bc}.sorted.bam
+#samtools index ${workDir}/bamFilesdb/${expName}_fail_${bc}.sorted.bam
+
+
+################################################
+# getting chr intervals
+################################################
+if [ ! -f "chrom.sizes" ]
+then
+        faidx $genomeFile -i chromsizes > chrom.sizes
+fi
+
+chrIntervals=( `cut -f1,2 chrom.sizes | sed $'s/\t/:1-/g'` )
+chr=( `cut -f1 chrom.sizes` )
+
+
+################################################
+# identifying CmG
+################################################
+echo "identify CmG ..."
+doFail=FALSE
+
+mkdir -p ${workDir}/meth_callsdb/
+
+for i in "${!chr[@]}"
+do
+	nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/dbbcFastq/pass/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_callsdb/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv
+	if [ "${doFail}" = "TRUE" ]
+	then
+		echo "processing failed reads"
+		nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/dbbcFastq/fail/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_callsdb/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv
+	fi
+done
+
+
+#### combine separate chromosomes into single file ####
+
+# first write header
+head -1 ${workDir}/meth_callsdb/${expName}_pass_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${expName}_pass_${bc}_CpGcalls.tsv
+if [ "${doFail}" = "TRUE" ]
+then
+	head -1 ${workDir}/meth_callsdb/${expName}_fail_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${expName}_fail_${bc}_CpGcalls.tsv
+fi
+
+
+# then combine files
+for i in "${!chr[@]}"
+do
+        tail -n +2 ${workDir}/meth_callsdb/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${expName}_pass_${bc}_CpGcalls.tsv
+	if [ "${doFail}" = "TRUE" ]
+	then
+        	tail -n +2 ${workDir}/meth_callsdb/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${expName}_fail_${bc}_CpGcalls.tsv
+	fi
+        rm ${workDir}/meth_callsdb/${expName}_????_${bc}_CpGcalls_${chr[$i]}.tsv
+done
+
+
+#### caclulating frequency ######
+mkdir -p ${workDir}/meth_freqdb
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${expName}_pass_${bc}_CpGcalls.tsv > ${workDir}/meth_freqdb/${expName}_pass_${bc}_freqCmG.tsv
+
+if [ "${doFail}" = "TRUE" ]
+then
+	${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${expName}_fail_${bc}_CpGcalls.tsv > ${workDir}/meth_freqdb/${expName}_fail_${bc}_freqCmG.tsv
+fi
+
+################################################
+# identifying GCm
+################################################
+echo "identify GCm ..."
+
+mkdir -p ${workDir}/meth_callsdb/
+
+for i in "${!chr[@]}"
+do
+	echo ${chr[$i]}
+	echo ${chrIntervals[$i]}
+	nanopolish call-methylation -t 4 -q gpc -r ${workDir}/dbbcFastq/pass/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${expName}_pass_${bc}.sorted.bam -g $genomeFile -w ${chrIntervals[$i]} > ${workDir}/meth_callsdb/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv
+
+	if [ "${doFail}" = "TRUE" ]
+	then
+		nanopolish call-methylation -t 4 -q gpc -r ${workDir}/dbbcFastq/fail/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${expName}_fail_${bc}.sorted.bam -g $genomeFile -w ${chrIntervals[$i]} > ${workDir}/meth_callsdb/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv
+	fi
+done
+
+
+#### combine separate chromosomes into single file ####
+
+# first write header
+head -1 ${workDir}/meth_callsdb/${expName}_pass_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${expName}_pass_${bc}_GpCcalls.tsv
+if [ "${doFail}" = "TRUE" ]
+then
+	head -1 ${workDir}/meth_callsdb/${expName}_fail_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${expName}_fail_${bc}_GpCcalls.tsv 
+fi
+
+# then combine files
+for i in "${!chr[@]}"
+do 
+	tail -n +2 ${workDir}/meth_callsdb/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${expName}_pass_${bc}_GpCcalls.tsv
+	if [ "${doFail}" = "TRUE" ]
+	then
+		tail -n +2 ${workDir}/meth_callsdb/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${expName}_fail_${bc}_GpCcalls.tsv
+	fi
+	rm ${workDir}/meth_callsdb/${expName}_????_${bc}_GpCcalls_${chr[$i]}.tsv
+done
+
+
+#### caclulating frequency ######
+mkdir -p ${workDir}/meth_freqdb
+
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${expName}_pass_${bc}_GpCcalls.tsv > ${workDir}/meth_freqdb/${expName}_pass_${bc}_freqGCm.tsv
+
+if [ "${doFail}" = "TRUE" ]
+then
+	${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${expName}_fail_${bc}_GpCcalls.tsv > ${workDir}/meth_freqdb/${expName}_fail_${bc}_freqGCm.tsv
+fi
+
diff --git a/alignFastqdb_spikeIn.sh b/alignFastqdb_spikeIn.sh
new file mode 100644
index 0000000..5221b3d
--- /dev/null
+++ b/alignFastqdb_spikeIn.sh
@@ -0,0 +1,126 @@
+#! /bin/bash
+## script to arrange all fastq files into batches for analysis. Combined files will be created for
+## each barcode of interest for both passed and failed reads (e.g. pass_barcode01 or fail_barcode01).  
+
+# Get variables from command line
+expName=$1 	# experiment name (date of exp usually)
+bc=$2 		# barcode
+genomeFile=$3 	# full path to reference genome
+genomeName=`basename $genomeFile`
+genomeName=${genomeName%.fasta}
+
+
+####### modules to load ##########
+module load vital-it
+#module load R/3.5.1
+module add UHTS/Analysis/minimap2/2.12;
+module add UHTS/Analysis/samtools/1.8;
+############################################
+
+
+
+
+#################################################
+## aligning to genome
+#################################################
+#
+#echo "aligning to genome..."
+#
+#mkdir -p ../bamFilesdb/${genomeName}
+#
+## map reads to genome with minimap2
+## filter reads with flag=2308: unmapped (4) + secondary alignment (256) + supplementary alignment (2048) [the latter category is the main problem]
+#minimap2 -ax map-ont $genomeFile ../dbbcFastq/pass/${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T tmp -o ../bamFilesdb/${genomeName}/${expName}_pass_${bc}.sorted.bam 
+#minimap2 -ax map-ont $genomeFile ../dbbcFastq/fail/${bc}.fastq.gz | samtools view -F 2308 -b | samtools sort -T tmp -o ../bamFilesdb/${genomeName}/${expName}_fail_${bc}.sorted.bam
+#
+#echo "index bam file ..."
+#samtools index ../bamFilesdb/${genomeName}/${expName}_pass_${bc}.sorted.bam
+#samtools index ../bamFilesdb/${genomeName}/${expName}_fail_${bc}.sorted.bam
+
+
+################################################
+# getting chr intervals
+################################################
+if [ ! -f "${genomeName}.chrom.sizes" ]
+then
+        faidx $genomeFile -i chromsizes > ${genomeName}.chrom.sizes
+fi
+
+chrIntervals=( `cut -f1,2 ${genomeName}.chrom.sizes | sed $'s/\t/:1-/g'` )
+chr=( `cut -f1 ${genomeName}.chrom.sizes` )
+
+
+
+################################################
+# identifying CmG
+################################################
+echo "identify CmG ..."
+
+mkdir -p ../meth_callsdb/${genomeName}
+for i in "${!chr[@]}"
+do
+${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/dbbcFastq/pass/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${genomeName}/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv
+
+#${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q cpg -w ${chrIntervals[$i]} -r ${workDir}/dbbcFastq/fail/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${genomeName}/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv
+done
+
+
+#### combine separate chromosomes into single file ####
+
+# first write header
+head -1 ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv
+#head -1 ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv
+
+# then combine files
+for i in "${!chr[@]}"
+do
+        tail -n +2 ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv
+ #       tail -n +2 ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_CpGcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv
+        rm ${workDir}/meth_callsdb/${genomeName}/${expName}_????_${bc}_CpGcalls_${chr[$i]}.tsv
+done
+
+
+#### caclulating frequency ######
+mkdir -p ../meth_freq/${genomeName}
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_CpGcalls.tsv > ${workDir}/meth_freqdb/${genomeName}/${expName}_pass_${bc}_freqCmG.tsv
+
+#${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_CpGcalls.tsv > ${workDir}/meth_freqdb/${genomeName}/${expName}_fail_${bc}_freqCmG.tsv
+
+
+
+################################################
+# identifying GCm
+################################################
+echo "identify GCm ..."
+
+mkdir -p ../meth_callsdb/${genomeName}
+for i in "${!chr[@]}"
+do
+${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -w ${chrIntervals[$i]} -r ${workDir}/dbbcFastq/pass/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${genomeName}/${expName}_pass_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv
+
+#${NANOPOLISH_DIR}/nanopolish call-methylation -t 4 -q gpc -w ${chrIntervals[$i]} -r ${workDir}/dbbcFastq/fail/${bc}.fastq.gz -b ${workDir}/bamFilesdb/${genomeName}/${expName}_fail_${bc}.sorted.bam -g $genomeFile > ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv
+done
+
+
+#### combine separate chromosomes into single file ####
+
+# first write header
+head -1 ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv
+#head -1 ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[0]}.tsv > ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv 
+
+# then combine files
+for i in "${!chr[@]}"
+do 
+    tail -n +2 ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv
+ #   tail -n +2 ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_GpCcalls_${chr[$i]}.tsv >> ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv
+    rm ${workDir}/meth_callsdb/${genomeName}/${expName}_????_${bc}_GpCcalls_${chr[$i]}.tsv
+done
+
+
+
+#### caclulating frequency ######
+mkdir -p ../meth_freqdb/${genomeName}
+${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${genomeName}/${expName}_pass_${bc}_GpCcalls.tsv > ${workDir}/meth_freqdb/${genomeName}/${expName}_pass_${bc}_freqGCm.tsv
+
+#${NANOPOLISH_DIR}/scripts/calculate_methylation_frequency.py -i ${workDir}/meth_callsdb/${genomeName}/${expName}_fail_${bc}_GpCcalls.tsv > ${workDir}/meth_freqdb/${genomeName}/${expName}_fail_${bc}_freqGCm.tsv
+
diff --git a/basecallAlbacore.sh b/basecallAlbacore.sh
deleted file mode 100755
index 203c98f..0000000
--- a/basecallAlbacore.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#! /bin/bash
-## script to basecall all fast5 in the folder one level up called fast5files and its recursive directories with albacore
-## uses barcoding
-## outputs 200,000 reads per fastq file (-q option)
-## does not use batch subdirectories (-n 0 option)
-## output will be in e.g: ../workspace/pass/barcode07/firstfastq.fastq
-
-
-source activate albacore_env
-
-read_fast5_basecaller.py --flowcell FLO-MIN106 --kit SQK-LSK108 --barcoding --output_format fastq -n 0 -q 200000 --input ../fast5files/ --recursive --save_path ../ --worker_threads 8
-
-##################
-# run MinIONQC
-#################
-
-module load vital-it
-module load R/3.5.1
-
-# create qc output directory
-qcDir=../fastqQC
-mkdir -p $qcDir
-
-echo "doing MinIONQC..."
-# run Minion_qc
-# source: https://github.com/roblanf/minion_qc
-
-source ./varSettings.sh
-mkdir -p ${qcDir}/MinIONQC
-
-Rscript ${MINIONQC} -i ../sequencing_summary.txt -o $qcDir
-
-mv ../*.png ${qcDir}/MinIONQC/
diff --git a/basecallGuppy.sh b/basecallGuppy.sh
index 21eb720..7a53aee 100755
--- a/basecallGuppy.sh
+++ b/basecallGuppy.sh
@@ -1,43 +1,83 @@
 #! /bin/bash
-## script to basecall all fast5 in the folder one level up called fast5files and its recursive directories with Guppy
+## script to basecall all fast5 in the folder called fast5files and its recursive directories with Guppy
 ## .bashrc should include location of bin directory inside Guppy directory and export it as ${GUPPYDIR}
 ## uses barcoding
-## outputs 200,000 reads per fastq file (-q option)
-## output will be in e.g: ../fastqFiles/pass/firstfastq.fastq
-## next the files are sorted by barcode and output to e.g ../bcFastq/pass/barcodeXX/firstfastq.fastq
-## pycoQC is run and results are in ../qc/pycoQC/pycoQC.html
+## output will be in e.g: ./fastqFiles/pass/firstfastq.fastq
+## next the files are sorted by barcode and output to e.g ./bcFastq/pass/barcodeXX.fastq.gz
+## pycoQC is run and results are in ./qc/pycoQC/pycoQC.html
 
 source ./varSettings.sh
-fullPath=`readlink -f ../`
 
-${GUPPYDIR}/guppy_basecaller --input_path ${fullPath}/fast5Files --save_path ${fullPath}/fastqFiles --flowcell FLO-MIN106 --kit SQK-LSK109 --records_per_fastq 200000 --recursive  --cpu_threads_per_caller 8 --qscore_filtering --min_qscore 3 
-#--num_callers
 
-#basecall passed files
-mkdir -p ../bcFastq/pass
-${GUPPYDIR}/guppy_barcoder -i ${fullPath}/fastqFiles/pass -s ${fullPath}/bcFastq/pass --barcode_kits EXP-NBD104 --worker_threads 8 --recursive -q 200000
+##################
+# basecall
+#################
+
+
+#guppy_basecaller --input_path ${dataDir}/fast5Files --save_path ${workDir}/fastqFiles --flowcell FLO-MIN106 --kit SQK-LSK109 --records_per_fastq 200000 --recursive  --qscore_filtering --min_qscore 3  --device auto  
 
-#basecall failed files
-mkdir -p ../bcFastq/fail
-${GUPPYDIR}/guppy_barcoder -i ${fullPath}/fastqFiles/fail -s ${fullPath}/bcFastq/fail --barcode_kits EXP-NBD104 --worker_threads 8 --recursive -q 200000
 
-#rm ../fastqFiles
+##################
+# call barcodes
+#################
+
+deepbinner classify --native ${dataDir}/fast5Files > ${workDir}/classifications
 
 
+##################
+# bin by barcode
+##################
+
+mkdir -p ${workDir}/dbbcFastq/pass
+mkdir -p ${workDir}/dbbcFastq/fail
+
+cat ${workDir}/fastqFiles/pass/* > ${workDir}/fastqFiles/pass/passed.fq
+cat ${workDir}/fastqFiles/fail/* > ${workDir}/fastqFiles/fail/failed.fq
+
+deepbinner classify --native ${dataDir}/fast5Files > ${workDir}/classifications
+
+
+deepbinner bin --classes ${workDir}/classifications --reads ${workDir}/fastqFiles/pass/passed.fq --out_dir ${workDir}/dbbcFastq/pass
+deepbinner bin --classes ${workDir}/classifications --reads ${workDir}/fastqFiles/fail/failed.fq --out_dir ${workDir}/dbbcFastq/fail
+
+#rm ${workDir}/fastqFiles/pass/passed.fq
+#rm ${workDir}/fastqFiles/fail/failed.fq
+
+
+
+###################
+## call barcodes
+##################
+
+#mkdir -p ${workDir}/bcFastq/pass
+#guppy_barcoder -i ${workDir}/fastqFiles/pass -s ${workDir}/bcFastq/pass --barcode_kits EXP-NBD104 --device auto  --recursive
+
+
+#mkdir -p ${workDir}/bcFastq/fail
+#guppy_barcoder -i ${workDir}/fastqFiles/fail -s ${workDir}/bcFastq/fail --barcode_kits EXP-NBD104 --device auto  --recursive
+
 ##################
 # run pycoQC
 #################
 
-source activate pycoQC
+#source ${HOME}/.bashrc
+#source ${CONDA_ACTIVATE}
+#conda activate pycoQC
 
 # create qc output directory
-qcDir=../qc
-mkdir -p $qcDir/pycoQC
+qcDir=${workDir}/qc
+mkdir -p ${qcDir}/pycoQC
 
 #https://github.com/a-slide/pycoQC
 
-pycoQC -f ${fullPath}/fastqFiles/sequencing_summary.txt -b ${fullPath}/bcFastq/pass/barcoding_summary.txt -o ${qcDir}/pycoQC/pycoQC_${expName}_pass.html --title "nanoDSMF "${expName}" passed reads" --min_pass_qual 3
+#pycoQC --summary_file ${workDir}/fastqFiles/sequencing_summary.txt --barcode_file ${workDir}/bcFastq/pass/barcoding_summary.txt -o ${qcDir}/pycoQC/pycoQC_${expName}_pass.html --min_pass_qual 3
+
+
+#pycoQC --summary_file ${workDir}/fastqFiles/sequencing_summary.txt --barcode_file ${workDir}/bcFastq/fail/barcoding_summary.txt -o ${qcDir}/pycoQC/pycoQC_${expName}_fail.html
+
+#conda deactivate
+
+#pycoQC --summary_file ${workDir}/fastqFiles/sequencing_summary.txt --barcode_file ${workDir}/bcFastq/pass/barcoding_summary.txt -o ${qcDir}/pycoQC/pycoQC_${expName}_pass.html --min_pass_qual 3
 
-pycoQC -f ${fullPath}/fastqFiles/sequencing_summary.txt -b ${fullPath}/bcFastq/fail/barcoding_summary.txt -o ${qcDir}/pycoQC/pycoQC_${expName}_fail.html --title "nanoDSMF "${expName}" failed reads" --min_pass_qual 3 
 
-source deactivate
+pycoQC --summary_file ${workDir}/fastqFiles/sequencing_summary.txt -o ${qcDir}/pycoQC/pycoQC_${expName}.html
diff --git a/varSettings_example.sh b/varSettings_example.sh
index a366708..ff18e6f 100644
--- a/varSettings_example.sh
+++ b/varSettings_example.sh
@@ -1,16 +1,29 @@
 #! /bin/bash
 
 # name of experiment
-expName="20171027"
+expName="20190411"
 
 # barcodes used in this experiment
-barcodesOfInterest=( barcode05 barcode06 barcode07 barcode08 )
+barcodesOfInterest=( barcode01 barcode02 barcode03 barcode04 barcode05 unclassified )
+# barcodes with non C.elegans DNA spike in
+bcWithSpikeIn=( barcode01 barcode05 unclassified )
+
 
 # location of reference genome file
-genomeFile=/data/projects/p025/Jenny/genomeVer/PCR_wPM28_32/PCR_wPM28_32.fasta
+#genomeFile=/data/projects/p025/Jenny/genomeVer/PCR_wPM28_32/PCR_wPM28_32.fasta
+genomeFile=/mnt/imaging.data/jsemple/genomeVer/ws265/c_elegans.PRJNA13758.WS265.genomic.fa
+
+# location of reference genomes for spiked-in DNA
+#lambdaFile="/home/ubelix/izb/semple/genomeVer/lambda/lambdaPhage.fasta"
+#phiXfile="home/ubelix/izb/semple/genomeVer/phiX/phiX.fasta"
+lambdaFile=/mnt/imaging.data/jsemple/genomeVer/lambda/lambdaPhage.fasta
+phiXfile=/mnt/imaging.data/jsemple/genomeVer/phiX/phiX.fasta
+
+dataDir=/mnt/imaging.data/jsemple/20190411_dSMFv021-025np_N2gw
+workDir=/home/jsemple/20190411_dSMFv021-025np_N2gw
 
 # location of MinION program
-MINIONQC=/home/pmeister/software/MinIONQC.R
+#MINIONQC=/home/pmeister/software/MinIONQC.R
 
 ########## don't edit below this line ###############
 # note: the .bashrc should point to the location of nanopolish with the variable