Changes between Version 59 and Version 60 of SOP/scRNA-seq

Timestamp:

08/08/24 11:45:22 (5 months ago)

Author:

gbell

Comment:

--

SOP/scRNA-seq

@@ -48 +48 @@
         * Filter the gtf to include only a subset of the annotated gene biotypes, for example,
 {{{ 
-bsub cellranger mkgtf Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.filtered.gtf --attribute=gene_biotype:protein_coding
+sbatch --partition=20 --job-name=mkgtf --mem=32G --wrap "cellranger mkgtf Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.filtered.gtf --attribute=gene_biotype:protein_coding"
 }}}
         * Create the cellranger index using a command such as
 {{{
-bsub cellranger mkref --genome=MyGenome --fasta=genome.fa --genes=Genes.filtered.gtf --ref-version=1.0
+sbatch --partition=20 --job-name=mkgtf --mem=32G --wrap "cellranger mkref --genome=MyGenome --fasta=genome.fa --genes=Genes.filtered.gtf --ref-version=1.0"
 }}}
       * Optional: How to create a STAR index with parameters different than the defaults 
@@ -61 +61 @@
       * Run the actual [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count 'cellranger count'] command using syntax like
 {{{
-bsub cellranger count --id=ID --fastqs=PATH --transcriptome=DIR --sample=SAMPLE_LIST --project=PROJECT
+sbatch --partition=20 --job-name=cr_count --mem=32G --wrap "cellranger count --id=ID --fastqs=PATH --transcriptome=DIR --sample=SAMPLE_LIST --project=PROJECT"
 }}}