ATAC-seq : which read length?

Question

[guillaume.rbt]

Hi all,

I'm starting a new project with ATAC-seq, a first for me.

I was wondering if anyone would have an opinion on the read length I should use for the sequencing. (After some reading it seems that it should be 50 or 75 bp, but i'm not sure which is the best option)

Thanks

Answer 1

[trausch]

My suggestion would be to sequence in paired-end mode at short read length (50 or 75bp is fine but not longer) because then the insert size is informative for nucleosome patterns and you have more options for footprint analyses.

[guillaume.rbt]

Ok thanks for the tip.

Answer 2

[ATpoint]

ATAC-seq is not fundamentally different from other DNA-seq experiments in that regard. The longer reads the better as the chance of unique mapping increases with read length. We typically do 2x75bp on a HiSeq3000 or 2x50 on Novaseq SP.

[guillaume.rbt]

Thank you for the information, I think I will also go for 2*75bp.