Question: ATAC Mapping rate
0
gravatar for rachanaj
23 months ago by
rachanaj0
rachanaj0 wrote:

Hi

My lab is going to work on ATAC for the first time and I have been asked as to what is amount of sequencing we need to do. We want to end up with 50million aligned reads. So my question is what is the ballpark mapping rate that is observed for ATAC data. We are planning on doing 100bp paired-end reads.

My search led to this post where it seems the mapping rate can vary between 50% to 90% (https://www.biostars.org/p/170294/). Any further light on what is generally seen would be helpful.

Thanks

mapping rate atac • 1.2k views
ADD COMMENTlink modified 23 months ago by datascientist28350 • written 23 months ago by rachanaj0

What species are you working with?

ADD REPLYlink written 23 months ago by Sinji2.7k

We think it will be mouse.

ADD REPLYlink written 23 months ago by rachanaj0
4
gravatar for datascientist28
23 months ago by
University of Washington
datascientist28350 wrote:

It has varied for me from study to study. A study we did in dogs had an alignment rate of 50-55%. While, another study we did in xenopus tropicalis had an alignment rate of 80-90%. It's unlikely that the organism has anything to do with these results, but just showing the variety of data we have gotten. I posted a question about this a while back that I think would be good for you to read. We discussed a lot of the pitfalls and problems one can come across when looking at ATAC output. C: What is the reason for trimming reads to 30 bp for ATAC-seq aligning?

Lastly, it's important to remember that a large proportion of your reads will align to the MT region. There are newer methods (example) that can deplete these reads depending upon your needs.

ADD COMMENTlink written 23 months ago by datascientist28350
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