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!
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
Seen: 1,421 times
Last updated: Aug 08 '17
