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Old 10-13-2017, 03:12 PM   #54
sk8bro
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Location: boston

Join Date: Feb 2012
Posts: 30
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Hi Brian,

So I've considered your 3 suggestions and Seal seems the path of least resistance. To separate sequences with 1 SNP of importance, in presence of other sequencing error SNPs the references need to be considered simultaneously or else which SNP is the important one gets lost.

So... i took approach of using BBsplit (to ensure the .95 minid/idfilter) that I want, and then took everything mapped as input to Seal (default except k=8, ambiguous=toss).

There are a few read pairs that are coming out as "Unmapped" in the Seal step, but they aligned with BBsplit. I looked at one and saw it has 1 SNP in each of F and R ~150 bp reads. Which Processing parameter do I need to change in order to "Map" this read pair?

Thx, Kate
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