Downsampling ATAC-seq BAM files
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12 weeks ago
Elise • 0

Hi all,

I have two ATAC datasets sequenced on two sequencers with different read depths. I would like to downsample the one with higher read depth to match that of the other dataset as we are observing batch effects following integration.

To my understanding, I need to shuffle the BAM files to equal depth, and then I'll need to convert the BAM files to a fragment file for the purposes of my analysis. Unfortunately, I have no experience dealing with this (only worked with RNA-seq before). If anyone is knowledgeable about the process and could elaborate on it, I would appreciate any insight.

Thank you in advance!

ATAC-seq • 393 views
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is this single-cell?

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Single-nucleus as a part of the 10x multiomics protocol, yes.

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