Syntax update

cellgeni · Jan 14, 2022 · c3979aa · c3979aa
1 parent 70a0bb6
commit c3979aa
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Showing 7 changed files with 62 additions and 6 deletions.
diff --git a/scripts/starsolo_3p_v1.sh b/scripts/starsolo_3p_v1.sh
@@ -44,7 +44,7 @@ STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R2 $R1 --runDirPerm All_
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloCBlen 14 --soloUMIstart 15 --soloUMIlen $UMILEN --soloStrand $STR \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ genes.tsv barcodes.tsv matrix.mtx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
 
 ## gzip all outputs
 cd output

diff --git a/scripts/starsolo_3p_v2.sh b/scripts/starsolo_3p_v2.sh
@@ -42,7 +42,7 @@ STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R2 $R1 --runDirPerm All_
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloUMIlen $UMILEN --soloStrand $STR \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ genes.tsv barcodes.tsv matrix.mtx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
 
 ## gzip all outputs
 cd output

diff --git a/scripts/starsolo_3p_v3.sh b/scripts/starsolo_3p_v3.sh
@@ -42,7 +42,7 @@ STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R2 $R1 --runDirPerm All_
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloUMIlen $UMILEN --soloStrand $STR \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ genes.tsv barcodes.tsv matrix.mtx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
 
 ## gzip all outputs
 cd output

diff --git a/scripts/starsolo_5p_v1.sh b/scripts/starsolo_5p_v1.sh
@@ -42,7 +42,7 @@ STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R2 $R1 --runDirPerm All_
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloUMIlen $UMILEN --soloStrand $STR \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ genes.tsv barcodes.tsv matrix.mtx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
 
 ## gzip all outputs
 cd output

diff --git a/scripts/starsolo_5p_v2.sh b/scripts/starsolo_5p_v2.sh
@@ -42,7 +42,7 @@ STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R2 $R1 --runDirPerm All_
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloUMIlen $UMILEN --soloStrand $STR \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ genes.tsv barcodes.tsv matrix.mtx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
 
 ## gzip all outputs
 cd output

diff --git a/scripts/starsolo_ss2.sh b/scripts/starsolo_ss2.sh
@@ -27,7 +27,7 @@ mkdir $TAG.solo.SS2 && cd $TAG.solo.SS2
 STAR --runThreadN $CPUS --genomeDir $REF --runDirPerm All_RWX --readFilesCommand zcat $SORTEDBAM \
      --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 \
      --soloType SmartSeq --readFilesManifest ../$TAG.manifest.tsv --soloUMIdedup Exact --soloStrand Unstranded \
-     --soloFeatures Gene GeneFull --soloOutFileNames output/ genes.tsv barcodes.tsv matrix.mtx
+     --soloFeatures Gene GeneFull --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
 
 echo "ALL DONE!"
 
diff --git a/scripts/starsolo_strt.sh b/scripts/starsolo_strt.sh
@@ -0,0 +1,56 @@
+#!/bin/bash -e 
+
+## newest version of the script uses STAR v2.7.9a with EM multimapper processing in STARsolo (but it's not on by default; turn this on with --soloMultiMappers EM)
+## velocyto extra processing also became unnecessary 
+
+## this is for STRT - very popular in China!
+
+TAG=$1
+if [[ $TAG == "" ]]
+then
+  >&2 echo "Usage: ./starsolo_strt.sh <sample_tag>"
+  >&2 echo "(make sure you set the correct REF, FQDIR, and SORTEDBAM/NOBAM variables)"
+  exit 1
+fi
+
+CPUS=16      ## typically bsub this into normal queue with 16 cores and 64 Gb RAM.   
+REF=/nfs/cellgeni/STAR/human/2020A/index  ## choose the appropriate reference 
+FQDIR=/lustre/scratch117/cellgen/cellgeni/TIC-starsolo/tic-1211/GSE142653/fastqs  ### change to the directory with fastq files/folders
+BC=/lustre/scratch117/cellgen/cellgeni/TIC-starsolo/tic-1211/GSE142653/96_barcodes.list
+UMILEN=8  ## need to change barcode length too 
+STR=Forward  ## 3' 10x
+
+## choose one of the two otions, depending on whether you need a BAM file 
+SORTEDBAM="--outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 2 --limitBAMsortRAM 60000000000 --outMultimapperOrder Random --runRNGseed 1 --outSAMattributes NH HI AS nM CB UB GX GN"
+NOBAM="--outSAMtype None"
+
+mkdir $TAG && cd $TAG
+## for multiple fastq files; change grep options according to your fastq file format 
+R1=`find $FQDIR/* | grep $TAG | grep "_f1.fastq.gz" | sort | tr '\n' ',' | sed "s/,$//g"`
+R2=`find $FQDIR/* | grep $TAG | grep "_r2.fastq.gz" | sort | tr '\n' ',' | sed "s/,$//g"`
+
+if [[ $R1 == "" || $R2 == "" ]]
+then
+  >&2 echo "No appropriate R1 or R2 read files was found for sample tag $TAG! Make sure you have set the correct FQDIR."
+  >&2 echo "Usage: ./starsolo_strt.sh <sample_tag>"
+  exit 1
+fi
+
+## note the switched R2 and R1 compared to 10x! R1 is biological read in STRT-seq
+STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R1 $R2 --runDirPerm All_RWX --readFilesCommand zcat $NOBAM \
+     --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloCBlen 8 --soloUMIstart 9 --soloUMIlen $UMILEN --soloStrand $STR \
+     --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
+     --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx
+
+## gzip all outputs
+cd output
+for i in Gene/raw Gene/filtered GeneFull/raw GeneFull/filtered Velocyto/raw Velocyto/filtered
+do 
+  cd $i; for j in *; do gzip $j & done
+  cd ../../
+done
+
+wait
+echo "ALL DONE!"
+