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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:
After receiving no alignments, and perusing the bowtie manual a bit more, I came up with this:
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.
Code:
bowtie -CS -k 2 --best <ebwt name> -f <csfasta_file> -Q <qual_file>
Code:
bowtie -CS --best -l 10 -e 100 -n 3 -k 2 <ebwt name> -f <csfasta_file> -Q <qual_file>