about Mapability and Blacklisted regions?

Question

[morovatunc]

HI,

I am using a GEO dataset which contains couple ChIP-seq peak files. (BEDs). To eleminate false discovery and low quality data, I would like to filter black listed regions (by DAC and Duke) and low mapability regions. I have couple questions related to this process.

1) For mapability which k-mer should I choose? (to be clear, If I use 100, will reviewer make problem ?)

Thank you for your help,

Best regards,

Tunc.

Answer 1

[Devon Ryan]

Choose whichever one closest matches your read length. In practice, no one bothers mentioning exactly which file they're using for this so I would be truly amazed if a reviewer even thought to wonder about this (I certainly wouldn't).

[morovatunc]

Thank you very much.