Exceptionally high peak/reads in ATACseq bam and peak files
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10 months ago
bright602 ▴ 40

Hi there, could anyone tell me how to remove the exceptionally high peak in the ATACseq? I got those high reads in both bam files and peak files? Thanks a lot!

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sequencing • 254 views
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Can you confirm that you have deduplicated the data and excluded the ENCODE blacklist regions?

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I removed the PCR duplicates through Picard. For the species I am working on, ENCODE does not have the blacklist regions yet.

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Did you set REMOVE_DUPLICATES parameter to true?

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yes, I did set the REMOVE_DUPLICATES=true

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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.

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Thanks, I have removed the mitochondrial reads too.

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