SEQanswers - View Single Post - Bowtie and reads that failed to align: (100.00%)

fkrueger · 01-26-2011, 01:43 AM

Hi michy,

The command you used looks ok-ish, but

(a) -q is the default, however Bowtie will then assume Phred33 qualities. The HiSeq seems to chuck out Phred64 encoded data though, try specifiying -q --phred64-quals
(b) -I 0 is not not required as it is the default
(c) If you still don't get any alignments you might want to increase -X to a higher value, maybe your insert sizes are just larger than 300bp?

Hope (a) or (c) will fix it.

01-26-2011, 01:43 AM	#2
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 625	Hi michy, The command you used looks ok-ish, but (a) -q is the default, however Bowtie will then assume Phred33 qualities. The HiSeq seems to chuck out Phred64 encoded data though, try specifiying -q --phred64-quals (b) -I 0 is not not required as it is the default (c) If you still don't get any alignments you might want to increase -X to a higher value, maybe your insert sizes are just larger than 300bp? Hope (a) or (c) will fix it.