Unexpected results for RNA-DNA Matching

[arual97]

Hello,

we are having issues with the quality control of the MAE module's RNA-DNA matching. Maybe you can help us figure out what's going wrong?

We use RNA and DNA from tumor tissue (a specific cancer) rather than normal tissue. According to the results, none of our samples match. The median proportion of matching is between 0.64 and 0.74. We have triple checked that the BAM and VCF pairs belong to the same person.

Could this be because we are using tumor samples instead of normal tissue? Or could it have something to do with the way the VCF files are filtered?

Thank you for your help!

[vyepez88]

Hi,
Yes, it could be due to having tumor samples there's a higher proportion of variants not present in both the DNA and RNA. Did you get to create the histogram with the matching rates? You should, nonetheless, be able to see 2 populations.

[arual97]

Hi,

thanks for the fast reply.
Yes, I have the histogram with the matching rates and there are two groups (see attachment).

[vyepez88]

Great to see. I wouldn't worry and suggest a cut-off of 0.675.

[arual97]

alright, thank you very much!