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Old 08-18-2014, 09:00 AM   #1
bioWizz
Junior Member
 
Location: Manipal

Join Date: Jul 2013
Posts: 6
Default Bismark for Ion Torrent

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
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