[mira_talk] assembling variants
- From: Fleur Darré <fleur.darre@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 01 Mar 2010 22:01:54 +0100
Hi,
I've been moving around my problem without finding an obvious solution.
I hope you'll be able to help me for this and thank you for this in advance.
I'm currently assembling solexa reads, mapping them against a given
virome. I hope to see some variability even INSIDE my sample and would
like to assess it.
My overall coverage is around 300, so, even if I have 10 to 20
haplo-virome (which I expect), it should be ok. (In another assembly, I
have a 25x coverage for a single expected strain)
Now, the (directed) assembly goes well, I end up with a single contig.
Some of the .exp files do correspond to several reads together (how
many? how deeply?). When I edit my output in Gap4 (staden package),
these long .exp files's quality are all set to 1, which provides unfair
excessive weight to the reads that were kept "alone". Even if I used the
Base Frequency as consensus algorithm (avoiding the weigth problem),
each isolated read has as an as heavy weight as a "long .exp"... which
is a strong bias when I want to assess the frequency of a given
variant/allele in my sample (for this purpose, I've been using different
consensus sequence out of gap4, with different cons threshold).
Am I missing some otpion? some step?
Is there a way to get the SNPs and there frequency (among reads) without
prior knowledge on strains?
Thanks again,
Fleur Darré
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