Add TRF in mouse BSgenome
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fusion.slope ▴ 10
@fusionslope-12296
Last seen 6.0 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
BSgenome.Mmusculus tandem repeats TRF • 1.2k views
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shepherl 4.1k
@lshep
Last seen 2 hours ago
United States

There are two different BSgenome packages for mm10, BSgenome.Mmusculus.UCSC.mm10.masked and BSgenome.Mmusculus.UCSC.mm10. Doesn't the BSgenome.Mmusculus.UCSC.mm10.masked have the information you are looking for?
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I do not think it does.

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Why do you think that? The help page says

Note
The masks in this BSgenome data package were made from the following source data files:
AGAPS masks: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz
RM masks: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromOut.tar.gz
TRF masks: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromTrf.tar.gz
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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.

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OK, there are instructions in the BSgenomeForge vignette in section 3that describe how to make one yourself. Does that not suffice?

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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.

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