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Set minimal reads length for Bowtie single-end alignment

Hi Everyone,

Is there a way to set minimal reads length for Bowtie (not Bowtie 2) single-end alignment? For example, I have a dataset with reads length range from 20 bp to 48bp after adaptor trimming, but I only want Bowtie to use reads length 25 bp to 48 bp to align to reference genome, is there a way to do this? I read Bowtie manual and I could not find an option. Perhaps the only way is that I need to trim the data first to 25 bp to 48 bp range and then use Bowtie?

Thanks,

Xiao

rna-seq
• 2,313 views • link
written by xiaoleiusc xiaoleiusc

You could use reformat.sh from BBMap suite to feed reads > 25 bp and < 48 bp to bowtie. 

$ reformat.sh in=your_reads.fq.gz out=stdout.fq.gz minlength=25 maxlength=48 | bowtie (read from stdin) .......

Remove .gz if your reads are not compressed from both in= and out=. If bowtie needs uncompressed reads, then only from out=.

• 0 views • link
written by GenoMax GenoMax

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