bc trim option to take as many ints as source files?
wheaton5 opened this issue · comments
For linked reads we want to trim 23 bases from R1 but not from R2. Right now I'm making two calls and then doing a Logex 'result = (A |+ B)' R1 R2.
This would be fine except for min counts on 2 files vs one file. Making a trim of 23 for both is okay except you do lose a fair amount of data. I can make this change and make a pull request if you are willing to take pull requests. Or i can just make this change in my forked version.
Let's discuss this afternoon on zoom as I don't quite understand. My
thought was that
you are building a relative profile of these reads relative to the
Haplex table to find
where the het- and hom-mers are in each of these paired Illumina reads.
So one can
be prefix trimmed, the other not, and the relative profiles paired in
the ensuing scan.
-- Gene
…On 4/12/21, 10:53 PM, Haynes Heaton wrote:
For linked reads we want to trim 23 bases from R1 but not from R2.
Right now I'm making two calls and then doing a Logex 'result = (A |+
B)' R1 R2.
This would be fine except for min counts on 2 files vs one file.
Making a trim of 23 for both is okay except you do lose a fair amount
of data. I can make this change and make a pull request if you are
willing to take pull requests. Or i can just make this change in my
forked version.
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I think we resolved this issue.