Question: about Mapability and Blacklisted regions?
0
gravatar for morovatunc
3.2 years ago by
morovatunc450
Turkey
morovatunc450 wrote:

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.

ucsc mapability • 806 views
ADD COMMENTlink modified 3.2 years ago by Devon Ryan95k • written 3.2 years ago by morovatunc450
3
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

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).

ADD COMMENTlink written 3.2 years ago by Devon Ryan95k

Thank you very much.

ADD REPLYlink written 3.2 years ago by morovatunc450
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