I am attempting to align a transcriptome sequenced with Hiseq to a reference using bowtie. The parameters I am using are:
bowtie -S -p 2 reference -q --phred64-quals
And none of the reads align. They also do not align if I do not include the quality parameter, or any modification such as the --ff suggested in related postings.
I have checked for adapter contamination and found very little, the reads were cleaned using ngs backbone, although I am not using that pipeline for anything downstream of cleaning. It has also been reported by some that they do not align in paired end but do in single end, my reads do not align in either case. Around 30% of the reas align in bwa.
Does anyone have any idea why this is the case?
Thanks!
Sarah
bowtie -S -p 2 reference -q --phred64-quals
And none of the reads align. They also do not align if I do not include the quality parameter, or any modification such as the --ff suggested in related postings.
I have checked for adapter contamination and found very little, the reads were cleaned using ngs backbone, although I am not using that pipeline for anything downstream of cleaning. It has also been reported by some that they do not align in paired end but do in single end, my reads do not align in either case. Around 30% of the reas align in bwa.
Does anyone have any idea why this is the case?
Thanks!
Sarah
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