Add TRF in mouse BSgenome
1
0
Entering edit mode
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 • 1.1k views
ADD COMMENT •
1
Entering edit mode
shepherl 4.1k
@lshep
Last seen 18 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?
ADD COMMENT •
0
Entering edit mode

I do not think it does.

ADD REPLY •
0
Entering edit mode

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
ADD REPLY •
0
Entering edit mode

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.

ADD REPLY •
0
Entering edit mode

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

ADD REPLY •
0
Entering edit mode

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.

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 538 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6