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.
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Question: genome mappability and peak calling
17 months ago by
Crevi • 0
Crevi • 0 wrote:
16 months ago by
Jennifer Hillman Jackson ♦ 25k
Jennifer Hillman Jackson ♦ 25k wrote:
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 COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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