Question: Run windowCounts only on annotated regions?
0
gravatar for endrebak85
2.2 years ago by
endrebak8530
endrebak8530 wrote:

I want to run windowCounts only on some annotated regions. Is this possible?

readParams has a discard-option, but not one for include...

Thanks. 

csaw • 334 views
ADD COMMENTlink modified 2.2 years ago by Aaron Lun23k • written 2.2 years ago by endrebak8530
Answer: Run windowCounts only on annotated regions?
2
gravatar for Aaron Lun
2.2 years ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

No. The closest you can get is to run windowCounts on the whole genome (or selected chromosomes), and then to apply findOverlaps to select windows that overlap your regions of interest. Depending on what you want to use the counts for, it may be more appropriate to construct bin/window intervals yourself and to apply regionCounts, e.g., as described in A: Use csaw to build matrix for heatmap?.

ADD COMMENTlink written 2.2 years ago by Aaron Lun23k

Thanks, csaw is wonderful.

ADD REPLYlink written 2.2 years ago by endrebak8530
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