Exceptionally high peak/reads in ATACseq bam and peak files
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Can you confirm that you have deduplicated the data and excluded the ENCODE blacklist regions?
I removed the PCR duplicates through Picard. For the species I am working on, ENCODE does not have the blacklist regions yet.
Did you set
REMOVE_DUPLICATES parameter to true?yes, I did set the REMOVE_DUPLICATES=true
Removed mitochondrial reads? Even if not I would ignore it and proceed with downstream analysis and only come back if you see odd things downstream.
Thanks, I have removed the mitochondrial reads too.