Question: ATAC-seq : which read length?
0
gravatar for guillaume.rbt
28 days ago by
guillaume.rbt540
France
guillaume.rbt540 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 • 123 views
ADD COMMENTlink modified 28 days ago • written 28 days ago by guillaume.rbt540
1
gravatar for trausch
28 days ago by
trausch1.2k
Germany
trausch1.2k 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 28 days ago by trausch1.2k

Ok thanks for the tip.

ADD REPLYlink written 28 days ago by guillaume.rbt540
1
gravatar for ATpoint
28 days ago by
ATpoint15k
Germany
ATpoint15k 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, usually aiming for about 20-50mio raw reads per sample depending on the number of samples and the scientific question.

ADD COMMENTlink written 28 days ago by ATpoint15k

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

ADD REPLYlink written 28 days ago by guillaume.rbt540
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