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Old 07-15-2016, 06:47 AM   #1
ThePresident
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Question Looking for structural variants with paired-end sequencing data

Hello community,

I am dealing with 150bp, paired-end, Illumina sequencing data from a relatively small bacterial genome (around 2MB). I would like to identify structural variants, specifically small genomic inversions compared to the reference sequence.

My reasoning here is that inversions should be recognizable with broken pairs of paired-end data, specifically those that are on the same orientation. Basically, paired-end mates are normally on both Forward and Reverse strand (FR), but if they align perfectly on the same strand (FF or RR) then I might be looking at genomic inversion in that part of the genome.

My question: How do I pool out read pairs that map to the same strand?

Thank you,
TP
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Old 07-28-2016, 05:19 AM   #2
ThePresident
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OK - just in case someone else is looking for the same thing: simply use --ff option in bowtie when aligning paired-end reads.

TP
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