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,