[Seqan-dev] Read trimming question
- From: John St John <johnthesaintjohn@gmail.com>
- To: seqan-dev@lists.fu-berlin.de
- Date: Sat, 8 Oct 2011 17:06:47 -0700
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: [Seqan-dev] Read trimming question
Hello, I am working on a quick re-write of an alignment based short-read trimmer I wrote in C using SeqAnn. So far things are going really well. I followed the Alignment tutorial on the trac wiki, and now I have an Alignment Graph of a global alignment where gaps at all ends of the two short sequences aren't penalized and gaps in the middle are treated harshly. So pictorially I have an alignment like this: Seq1: ----ACATAG Seq2: TTAGATA--- I want to output the following trimmed sequences: Seq1: ACA Seq2: ATA However if the above alignment were reversed: Seq1: TTAGATA--- Seq2: ----ACATAG Then I want to output the merged and extended consensus, where I call mismatches using a seperate quality score string as a tie breaker. Basically I don't know how to traverse the Alignment Graph to pull out the information I need. I need to keep track of which sequence is which in the alignment graph so that I can deal with the above two cases properly. Any help or at least a link to a good resource on traversing an alignment graph and doing something similar would be greatly appreciated. I need to keep track of the indices of the bases I trim so that I can also output the trimmed or merged quality string. Thanks everyone for your time, -John |
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