Change BAM/unmapped read fastq options

cellgeni · Feb 14, 2025 · 2ad6fea · 2ad6fea
1 parent b80355c
commit 2ad6fea
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/scripts/starsolo_10x_auto.sh b/scripts/starsolo_10x_auto.sh
@@ -5,7 +5,7 @@
 ## in STARsolo which on by default; the extra matrix can be found in /raw subdir 
 
 SIF="/nfs/cellgeni/singularity/images/reprocess_10x.sif"
-CMD="singularity run --bind /nfs,/lustre $SIF"
+CMD="singularity run --bind /nfs,/lustre,/software $SIF"
 
 FQDIR=$1
 SERIES=$2
@@ -41,8 +41,8 @@ REF=/nfs/cellgeni/STAR/$SHORTSP/2020A/index                               ## cho
 WL=/nfs/cellgeni/STAR/whitelists                                       ## directory with all barcode whitelists
 
 ## choose one of the two otions, depending on whether you need a BAM file 
-#BAM="--outSAMtype BAM SortedByCoordinate --outBAMsortingBinsN 500 --limitBAMsortRAM 60000000000 --outMultimapperOrder Random --runRNGseed 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY GX GN"
-BAM="--outSAMtype None"
+#BAM="--outSAMtype BAM SortedByCoordinate --outBAMsortingBinsN 500 --limitBAMsortRAM 60000000000 --outSAMunmapped Within --outMultimapperOrder Random --runRNGseed 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY GX GN"
+BAM="--outSAMtype None --outReadsUnmapped Fastx"
 
 ###################################################################### DONT CHANGE OPTIONS BELOW THIS LINE ##############################################################################################
 
@@ -268,13 +268,13 @@ then
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloCBstart 1 --soloCBlen $CBLEN --soloUMIstart $((CBLEN+1)) --soloUMIlen $UMILEN --soloStrand Forward \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --outFilterScoreMin 30 --genomeLoad LoadAndRemove \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx --soloMultiMappers EM --outReadsUnmapped Fastx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx --soloMultiMappers EM
 else 
   $CMD STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn $R2 $R1 --runDirPerm All_RWX $GZIP $BAM \
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloCBlen $CBLEN --soloUMIstart $((CBLEN+1)) --soloUMIlen $UMILEN --soloStrand $STRAND \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 --genomeLoad LoadAndRemove \
-     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx --soloMultiMappers EM --outReadsUnmapped Fastx
+     --soloFeatures Gene GeneFull Velocyto --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx --soloMultiMappers EM
 fi
 
 ## index the BAM file