Question: ATAC-seq : which read length?
0
gravatar for guillaume.rbt
6 months ago by
guillaume.rbt650
France
guillaume.rbt650 wrote:

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

sequencing atac-seq • 660 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by guillaume.rbt650
1
gravatar for trausch
6 months ago by
trausch1.4k
Germany
trausch1.4k wrote:

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.

ADD COMMENTlink written 6 months ago by trausch1.4k

Ok thanks for the tip.

ADD REPLYlink written 6 months ago by guillaume.rbt650
1
gravatar for ATpoint
6 months ago by
ATpoint24k
Germany
ATpoint24k wrote:

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.

ADD COMMENTlink modified 12 weeks ago • written 6 months ago by ATpoint24k

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

ADD REPLYlink written 6 months ago by guillaume.rbt650
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