To perform gc content bias corrections between atac-seq technical replicates

Question

[hyunjeong]

Hi

I am conducting an atac-seq data analysis.

I would like to proceed with the GC content bias correction in atac-seq data between the three replicates.

I would like to proceed with ComputeGCBias and CorrectGCBias of deeptools or after conducting GC content bias correction based on peak region in the count file.

How are you guys progressing? Is there the best way you've ever done it?

Also, I wonder if you removed the batch effect together using SVA-seq or Combat after gc content bias correction.

I need your advice.

Thank you!