Question: genome mappability and peak calling
0
gravatar for Crevi
5 months ago by
Crevi0
Crevi0 wrote:

I am working with a brassica plant that it is not the model Arabidopsis thaliana. How important is to know the genome mappability of the exact genome to perform MACS2 or SICER peak calling? Can I estimate it form the size of the genome and the % of repetitive elements? Any help will be appreciated.

alignment chip-seq • 188 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by Crevi0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Using the score for A. thaliana might be ok but finding out exactly from a source that understands your genome would be better, and this forum is not the best place for that advice. Brassica can be quite divergent. Subtracting repetitive elements are probably not enough but you could test that out versus A. thaliana and examine the differences.

Specific advice for MACS and estimated genome size was given in this prior Q&A: https://www.biostars.org/p/178995/#178998

If you want to try to estimate the effective genome size on your own in a more specific way, that same forum has much advice about how others are doing this.

Best, Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson23k
0
gravatar for Crevi
5 months ago by
Crevi0
Crevi0 wrote:

Thanks, I am interested in knowing who critical is the "genome mappability value" in MACS2 and the link provided answer some of my quiestion.

ADD COMMENTlink written 5 months ago by Crevi0
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