Changes between Version 10 and Version 11 of SOPs/rna-seq-diff-expressions_TE

Timestamp:

10/30/25 15:43:22 (4 days ago)

Author:

kdesilva

Comment:

--

SOPs/rna-seq-diff-expressions_TE

@@ -13 +13 @@
 
 {{{
-bsub STAR --genomeDir /path/to/STAR/index/for/organism --readFilesIn /path/to/reads_1.fastq.gz /path/to/reads_2.fastq.gz --outFileNamePrefix somePrefix --sjdbScore 2 --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100
+sbatch --job-name=STAR_align --mem=32G --wrap="STAR --genomeDir /path/to/STAR/index/for/organism --readFilesIn /path/to/reads_1.fastq.gz /path/to/reads_2.fastq.gz --outFileNamePrefix somePrefix --sjdbScore 2 --runThreadN 8 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100"
 }}}
 
@@ -24 +24 @@
 {{{
 # Reverse stranded reads
-bsub TEcount --sortByPos --format BAM --stranded reverse -b /path/to/alignment.bam --GTF /path/to/gene.gtf --TE /path/to/TE.gtf --mode multi --project projectName -i 100
+sbatch --job-name=TEcount --mem=16G --wrap="TEcount --sortByPos --format BAM --stranded reverse -b /path/to/alignment.bam --GTF /path/to/gene.gtf --TE /path/to/TE.gtf --mode multi --project projectName -i 100"
 }}}