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fusion.slope
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@fusionslope-12296
Last seen 5.9 years ago
Hello,
I am wondering if there is any way to add the TRF mask of the tandom repeat regions in the mouse mm10 BSgenome object. Is there a way to do that?
Thanks in advance
I do not think it does.
Why do you think that? The help page says
That's for hg19, and we need mm10 (https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Mmusculus.UCSC.mm10.masked.html). The mm10 BSgenome does have the AGAPS masks, but it does not seem to have the TRF masks.
OK, there are instructions in the BSgenomeForge vignette in section 3that describe how to make one yourself. Does that not suffice?
I think that there are. Thanks for the tip! It seems like the TRF masks fro mm10 can be found on this site: https://tandem.bu.edu/trf/trf.html.