EDIT: Repeat region drop out

Question

[skbrimer]

Hello everyone,

I have a quick question. I have what looks like a drop out in a repeat region of our genome of interest. I was wondering if it is a possible deletion or if it's just an artifact of repeat handling by the aligner. I understand from a biological stand point I need to primer across it to confirm, however I'm interested in how do I determine if its an actual possible deletion or an aligner issue.

Is it possible to tell from the data or because it is a repeat region is it not possible?

https://drive.google.com/file/d/0B6NiSc5ahjxWc3kyRDUzZGtpZGc/view?usp=sharing

EDIT:

I apologize, this is an Ion Torrent single end data set so I do not have any paired end data.

[Devon Ryan]

That looks more like an artefact, but to be sure see if the reads aligning on either side have soft-clipped regions that might span over the repeat. If they don't (and whatever aligner you used allowed soft-clipping), then it's just an artefact.

[skbrimer]

So if the reads are soft-clipped then it could indicate a deletion?

[Devon Ryan]

Correct, at least if the soft-clipped sequence maps to the other side of the low coverage region. To me, that just looks like a repeat or low complexity region.

[skbrimer]

Thank you for the clarification, Devon!