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Old 12-12-2014, 02:17 PM   #1
tomas.fer
Junior Member
 
Location: Prague

Join Date: Feb 2013
Posts: 1
Post Extraction of (two) sequence variants from exons

Hi,
I mapped reads (150 bp) to exon reference (in Geneious) and it is apparent that there are two different types of sequences, probably paralogues, each with high coverage (see attachment). Making consensus does not make sense in this case, sequences will be used for phylogeny and paralogs can destroy true signal etc.
Is there any possibility how to extract these two sequences/paralogues from mapped reads, i.e. make an alignment (actually two alignments...) from these reads belonging only to particular variant.
I prefer some possibility that allows for streaming as I have several thousands of such loci (of course not all of them have two or more "paralogues").
Thanks for some suggestions or links.
Tomas
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bam, pipeline, sam, variant detection, variant sequence

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