Changes between Version 16 and Version 17 of SOPs/rna-seq-diff-expressions

Timestamp:

01/15/14 14:30:28 (11 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -36 +36 @@
          * Note that htseq-count assumes that your reads are strand-specific, so if not, include "--stranded=no" (or half of your reads won't be counted).     
          * 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:
+         * For paired-end reads the sam file has to be sorted by read name with a command like this:
          * ''bsub  "samtools sort -n -m 5G accepted_hits.bam accepted_hitsSortedByname"''
          * To request a certain amount of memory and a specific node use ''bsub  -R "rusage[mem=50000]" -m NodeName ''