Changes between Version 65 and Version 66 of SOPs/rna-seq-diff-expressions

Timestamp:

09/02/25 09:37:53 (6 weeks ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -75 +75 @@
 
 #For PE reads the bam files needs to be sorted by name (default for htseq-count), eg.
-#bsub "samtools sort -n -o accepted_hits.sortedByName.bam -m 5G -O bam -T temp accepted_hits.bam"
+#sbatch --partition=20 --job-name=sort --mem=32G --wrap "samtools sort -n -o accepted_hits.sortedByName.bam -m 5G -O bam -T temp accepted_hits.bam"
 #If the bam file is sorted by coordinate you may try htseq-count -r option, eg. -r pos , however, 
 #this may not always work (htseq-count throws numerous errors).
-
-#To request a certain amount of memory and a specific node use bsub -R "rusage[mem=50000]" -m NodeName
  
 }}}
@@ -95 +93 @@
         * To quantify transcripts and genes in a GTF file, use a command like 
 {{{
-bsub cufflinks -G gene_models.gtf accepted_hits.bam
+sbatch --partition=20 --job-name=cuff --mem=32G --wrap "cufflinks -G gene_models.gtf accepted_hits.bam"
 }}}
         * To quantify transcripts, potentially novel, annotated by cufflinks, use a command like 
 {{{
-bsub cufflinks accepted_hits.bam
+sbatch --partition=20 --job-name=cuff --mem=32G --wrap "cufflinks accepted_hits.bam"
 }}}
         * Gene-level FPKM values are calculated by taking the sum of all transcript FPKMs for a gene.  As a result, no "gene length" needs to be calculated.
-        * NOTE: Some genes, although present in a GTF annotation file, may not get quantified by cufflinks.  This occurs for genes found in very long regions of overlapping genes (which exceed the default value for --max-bundle-length).  When this occurs, the standard err output of cufflinks (contained in the long LSF email when cufflinks is run via 'bsub') will contain the message "Warning: Skipping large bundle."  To correct this (or prevent it in the first place), add an argument like '--max-bundle-length 10000000' to the cufflinks command. You may want to compare the list of genes in the GTF file to that of the cufflinks output to verify that they match.
+        * NOTE: Some genes, although present in a GTF annotation file, may not get quantified by cufflinks.  This occurs for genes found in very long regions of overlapping genes (which exceed the default value for --max-bundle-length).  When this occurs, the standard err output of cufflinks (contained in the long slurm output when cufflinks is run via 'sbatch') will contain the message "Warning: Skipping large bundle."  To correct this (or prevent it in the first place), add an argument like '--max-bundle-length 10000000' to the cufflinks command. You may want to compare the list of genes in the GTF file to that of the cufflinks output to verify that they match.
         * If you only want to quantify genes in your GTF file use the -G option (instead of -g which will give also transcripts found by Cufflinks and will take away counts from transcripts in your gtf file).
 {{{