[BioC] Where is DEXSeq bioconductor package?
anders at embl.de
Thu Aug 4 18:19:18 CEST 2011
On 08/04/2011 06:11 PM, Fabrice Tourre wrote:
>>> It seems that BWA convert all the reads to forward strand, so I set -s
>>> yes. Is it right?
The SAM format specifies that for reads mapped to the reverse strand,
not the sequenced read but its reverse complement is stored.
However, the '-s' switch has nothing to do with this. It is about
whether you data is strand-specific, i.e., whether the strand to which a
read has been aligned is the template strand of the actual transcript.
(In standard RNA-Seq, the strand information is lost; newer protocols
preserve it by ligating adapters before rather than after second-strand
synthesis. The counting script needs to know which type of protocol you
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