Changes between Version 6 and Version 7 of SOPs/AssemblingRNAseqReads

Timestamp:

10/30/25 15:53:55 (4 days ago)

Author:

kdesilva

Comment:

--

SOPs/AssemblingRNAseqReads

@@ -14 +14 @@
  
 {{{
-bsub "inchworm --reads reads_sequence.fa --run_inchworm -K 25 --DS --min_assembly_coverage 5 > reads.inchworm_contigs.fa"
+sbatch --job-name=inchworm --mem=32G --wrap="inchworm --reads reads_sequence.fa --run_inchworm -K 25 --DS --min_assembly_coverage 5 > reads.inchworm_contigs.fa"
 }}}
       
@@ -32 +32 @@
 
 {{{
-  bsub cufflinks -M Mus_musculus.NCBIM37.62.noNT.rRNA.chrM.gtf sample1/accepted_hits.bam
-  bsub cufflinks -M Mus_musculus.NCBIM37.62.noNT.rRNA.chrM.gtf sample2/accepted_hits.bam
+  sbatch --job-name=cufflinks_s1 --mem=32G --wrap="cufflinks -M Mus_musculus.NCBIM37.62.noNT.rRNA.chrM.gtf sample1/accepted_hits.bam"
+  sbatch --job-name=cufflinks_s2 --mem=32G --wrap="cufflinks -M Mus_musculus.NCBIM37.62.noNT.rRNA.chrM.gtf sample2/accepted_hits.bam"
 }}}
 
@@ -73 +73 @@
 {{{
   Sample command: 
-  bsub tgicl contig_cleaned.fa -l 40 -p 90
+  sbatch --job-name=tgicl --mem=16G --wrap="tgicl contig_cleaned.fa -l 40 -p 90"
 }}}
 
@@ -83 +83 @@
 {{{
 # Sample command: In this example, contig.fa is the output file from above assembly step
-bsub "seqclean contig.fa -v /nfs/genomes/UniVec/UniVec_Core -o contig_cleaned.fa"
+sbatch --job-name=seqclean --mem=8G --wrap="seqclean contig.fa -v /nfs/genomes/UniVec/UniVec_Core -o contig_cleaned.fa"
 }}}