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Tandem duplications in Illumina's paired end data

asked 2017-05-16 07:56:40 -0600

updated 2017-05-16 11:05:13 -0600

Hi, I have 2 files on display at a single exon (paired-end pile-ups). One sample has a dup (probably tandem) while the other is control. I cannot recognize any difference in stacking patterns or read orientations. Are there any clues in the pile-up view that may indicate a presence of a short tandem dup (besides comparing depth)? Thanks!

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answered 2017-08-08 14:21:18 -0600

Hey Michael,

One mode that might be useful is to change the stacking mode to Paired End. If there is a tandem duplication, you may see it in the boundaries where paired-end reads that span it don't find the standard distribution for distance between the paired end reads or if there is an inversion you don't see one of a forward and reverse strand being paired.

Click the little gear icon in the GB Pile-up plot and switch Stack mode to Paired End.

I hope that helps! Happy hunting! Gabe

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Asked: 2017-05-16 07:56:40 -0600

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Last updated: Aug 08