Changes between Version 22 and Version 23 of SOPs/rna-seq-diff-expressions

Timestamp:

03/12/15 14:55:29 (10 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -32 +32 @@
       * Carefully choose the best "mode" to handle reads that don't completely map to exactly one gene
       * Counting can be also performed transcript level but this may be too much information
-      * htseq-count typically uses a SAM file as input, but a BAM fine can be used in place, for example
-         * ''samtools view accepted_hits.bam | htseq-count -m intersection-strict --stranded=no - gene_models.gtf >| gene_model.counts.txt''
+      * htseq-count can accept SAM or BAM (-f option), for example
+         * ''htseq-count -f bam -m intersection-strict --stranded=no accepted_hits.bam gene_models.gtf >| gene_model.counts.txt''
          * 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 with a command like this:
-         * ''bsub  "samtools sort -n -m 5G accepted_hits.bam accepted_hitsSortedByname"''
+         * Note the "-" can be used for input from standard input (stdin)
+         * For paired-end reads the sam file has to be sorted by read name, or coordinate, eg. ''bsub  "samtools sort -n -o accepted_hits.sortedByName.bam -m 5G -O bam -T temp accepted_hits.bam"''
          * To request a certain amount of memory and a specific node use ''bsub  -R "rusage[mem=50000]" -m NodeName '' 
     * Remove the rows at the bottom with descriptions like no_feature, ambiguous, etc.