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Old 05-10-2010, 03:44 AM   #1
Location: Jerusalem

Join Date: May 2010
Posts: 26
Default Recommended Bowtie Parameters

I'm attempting an alignment using bowtie with SOLiD results, based on 50bp reads. Using the following parameters, I got 100% no alignments despite knowing that alignments exist:

bowtie -CS -k 2 --best <ebwt name> -f <csfasta_file> -Q <qual_file>
After receiving no alignments, and perusing the bowtie manual a bit more, I came up with this:
bowtie -CS --best -l 10 -e 100 -n 3 -k 2 <ebwt name> -f <csfasta_file> -Q <qual_file>
This run has yet to complete, but it is getting a lot more alignments. I wanted to know if the parameters I used the second time are sensible, or if they're too permissive. Since I'm new to this, I have trouble gauging what might be too permissive. Also, I'm not sure I understand the -e option as explained in the bowtie manual - if anyone has a better explanation, it'd be appreciated.

Last edited by agc; 05-10-2010 at 03:46 AM.
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bowtie, solid

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