[BioC] Where is DEXSeq bioconductor package?

Simon Anders 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 
have used.)


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