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about Mapability and Blacklisted regions?

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.

mapability ucsc
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updated by Devon Ryan Devon Ryan • written by morovatunc morovatunc

1 answer

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).

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written by Devon Ryan Devon Ryan

Thank you very much.

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written by morovatunc morovatunc

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