This sequence is a simple repeat identical to its own complement (not reverse-complement) when shifted by two positions, which makes me suspicious. Just a general suspicion, though; I can't identify any culprits. If not for dpryan's extraordinary diligence in analyzing the raw data I would have thought it was a software problem. But since that seems to have been ruled out, I wonder if the self-complementary nature might be important. Have you tried aligning read1 and read2 independently to the reference, to see if in that context, read2 might map without soft-clipping?
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It still could be base caller software (RTA) that creates BCL files. This is more likely if the run was paused and restarted or the available disk space was limited sometime during run.
PS. Since only a subset of reads have been affected it might be useful to check if they are from the same tile or random.Last edited by nucacidhunter; 01-28-2017, 09:26 PM.Comment
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@nucaidhunter: They're from multiple lanes even. That's what makes it all so weird.
@Brian: Read 1 will align very well, read 2 will only align with soft-clipping.Comment
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