Question: Set minimal reads length for Bowtie single-end alignment
gravatar for xiaoleiusc
18 months ago by
USA/New York/The Rockefeller University
xiaoleiusc70 wrote:

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?



rna-seq • 536 views
ADD COMMENTlink written 18 months ago by xiaoleiusc70

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

$ 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=.

ADD REPLYlink modified 18 months ago • written 18 months ago by GenoMax96k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1121 users visited in the last hour