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
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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