Changes between Version 6 and Version 7 of SOPs/rna-seq-diff-expressions

Timestamp:

06/27/13 12:43:09 (12 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -38 +38 @@
          * Note the "-" before the gtf filename; this indicates that the SAM file is coming from standard input (in this case, piped from samtools).
          * For paired-end reads the sam file has to be sorted by read name. You can sort first the BAM file and then run htseq-count like this:
-         * ''bsub  "samtools sort -n -m 5000000000 accepted_hits.bam accepted_hitsSortedByname"''
+         * ''bsub  "samtools sort -n -m 5G accepted_hits.bam accepted_hitsSortedByname"''
          * ''bsub  "samtools view accepted_hitsSortedByname.bam | htseq-count -m intersection-strict --stranded=no - gene_models.gtf >| gene_model.counts.txt"''
     * Remove the rows at the bottom with descriptions like no_feature, ambiguous, etc.