I am trying to use Bismark on targeted bisulphite sequencing done on PGM. Average read length is about ~102 maximum being ~190.
Bismark uses bowtie2 and running it with varying parameters gives me aa lignment score of 8 - 10 % which is very low. When I use TMAP on torrent suite to map to converted reference sequence, I get decent alignment percentage.
Any suggestions on bowtie2 parameters for Ion Torrent variable read length data? Suggestion on analysis of targeted bisulphite sequencing with PGM output will also do.
Thanks
Bismark uses bowtie2 and running it with varying parameters gives me aa lignment score of 8 - 10 % which is very low. When I use TMAP on torrent suite to map to converted reference sequence, I get decent alignment percentage.
Any suggestions on bowtie2 parameters for Ion Torrent variable read length data? Suggestion on analysis of targeted bisulphite sequencing with PGM output will also do.
Thanks
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