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BnaT 12-18-2014 05:42 AM

Soft-clipping resequencing panel
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Hello guys,
I have some issues to understand the soft-clipped reads. I am analyzing a targeted resequencing panel. I trimmed the FASTQs, but I found very few trimmed bases. From a bam file, I have selected the reads that could point to a L breakpoint in a SV (e.g 120M31S). So, when I visualize them on the IGV I see that most of them have similar soft-clipped sequence at the end (pic attached), and this is repeated along the exon.
Does anyone have any idea of what could be happening? :confused:


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