Fixed typo in starsolo_10x_auto.sh, Farm memory request update (128 -…

…> 64 Gb), updated README

README.md

@@ -35,7 +35,7 @@ Once you have downloaded the needed fasta and GTF files, and applied the necessa
 All **CellGenIT** pre-made `STAR` references are located in `/nfs/cellgeni/STAR/`. Barcode whitelist files are located in `/nfs/cellgeni/STAR/whitelists`. 
 ## Resource requirements 
 
-By default, all processing is done using 16 CPUs and 128 Gb of RAM. Using the latest settings, you _should_ be able to process most 10x experiments with 64 Gb of RAM even when you need a sorted BAM output. Farm typically has ~8 Gb of RAM per core, so 8 CPUs/64 Gb RAM, or 16 CPUs/128 Gb RAM is probably optimal. 
+By default, all processing is done using 16 CPUs and 128 Gb of RAM (**UPD: 16 CPUs/64 Gb RAM as of January 22nd, 2024**). Using the latest settings, you _should_ be able to process most 10x experiments with 64 Gb of RAM even when you need a sorted BAM output. Farm typically has ~8 Gb of RAM per core, so 8 CPUs/64 Gb RAM, or 16 CPUs/128 Gb RAM is probably optimal. 
 
 ## Processing scRNA-seq with STARsolo
 

scripts/bsub16.sh

@@ -10,7 +10,7 @@ TAG=`basename $TAG`
 
 GROUP=`bugroup -w | grep "\b${USER}\b" | cut -d" " -f1`
 CPUS=16
-RAM=128000 
+RAM=64000 
 QUE="normal"
 WDIR=`pwd`
 

scripts/starsolo_10x_auto.sh

@@ -189,7 +189,7 @@ $CMD STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn test.R2.fastq test.R
      --soloUMIlen $UMILEN --soloStrand Forward \
      --soloUMIdedup 1MM_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \
      --soloCellFilter EmptyDrops_CR --clipAdapterType CellRanger4 --outFilterScoreMin 30 \
-     --soloFeatures Gene GeneFull --soloOutFileNames test_strand/ features.tsv barcodes.tsv matrix.mtx &> /dev/null 
+     --soloFeatures Gene GeneFull --soloOutFileNames test_forward/ features.tsv barcodes.tsv matrix.mtx &> /dev/null 
 
 $CMD STAR --runThreadN $CPUS --genomeDir $REF --readFilesIn test.R2.fastq test.R1.fastq --runDirPerm All_RWX --outSAMtype None \
      --soloType CB_UMI_Simple --soloCBwhitelist $BC --soloBarcodeReadLength 0 --soloCBlen $CBLEN --soloUMIstart $((CBLEN+1)) \