Question: How can I get the repbase and the repeatMasker versions that used in UCSC Web browser
0
gravatar for M K
3.7 years ago by
M K490
United States
M K490 wrote:

I downloaded some repeatMasker files for some species from UCSC web browser (i.e. rmsk files for mouse mm10, human hg19, ..etc.). My questions here how can I know the repbase and repeatMasker versions that used to create those files.

ADD COMMENTlink modified 3.7 years ago by Emily_Ensembl20k • written 3.7 years ago by M K490
0
gravatar for ablanchetcohen
3.7 years ago by
ablanchetcohen1.2k
Canada
ablanchetcohen1.2k wrote:

"UCSC uses the latest versions of RepeatMasker and repeat libraries available on the date when the assembly data is processed. RepeatMasker version information can usually be found in the README text for the assembly's bigZips downloads directory.

Masking is done using the RepeatMasker -s flag. For mouse repeats, we also use -m. In addition to RepeatMasker, we use the Tandem Repeat Finder (trf) program, masking out repeats of period 12 or less. The repeats are just "soft" masked. Alignments are allowed to extend through repeats, but not initiate in them."

https://genome.ucsc.edu/FAQ/FAQdownloads.html#download16

ADD COMMENTlink written 3.7 years ago by ablanchetcohen1.2k

I got it. Thanks ablanchetcohen for you help.

ADD REPLYlink written 3.7 years ago by M K490
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