Hello there,
I use Bowtie to map RNA-Seq reads to an algae genome. When I look at the read coverage for + and - strand separately I notice that there is expression on both strands in about the same places. That would be pretty efficient use of the genome. So I was wondering whether anybody has any experience with this and can tell me how reliable the +/- strand information from Bowtie is.
I cross checked my results with BWA, the results are very similar.
There is still the possibility that I mis-interpret the strand information in the sam output files.
Thanks in advance.
I use Bowtie to map RNA-Seq reads to an algae genome. When I look at the read coverage for + and - strand separately I notice that there is expression on both strands in about the same places. That would be pretty efficient use of the genome. So I was wondering whether anybody has any experience with this and can tell me how reliable the +/- strand information from Bowtie is.
I cross checked my results with BWA, the results are very similar.
There is still the possibility that I mis-interpret the strand information in the sam output files.
Thanks in advance.
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