Question

Soft Masked Version Of Hs37D5 Reference

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10.7 years ago

Daniel Gerlach ▴ 30

Hi,

I am working with the hs37d5 reference assembly from the 1000 human genome project. For some downstream analysis I would need a FASTA version of the file with repeats soft masked by Repeat Masker as lower case letters. Can I produce such a file or download it already?

Cheers, Daniel

fasta 1000genomes • 3.7k views

ADD COMMENT • link updated 3.4 years ago by AshNY • 0 • written 10.7 years ago by Daniel Gerlach ▴ 30

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Hi, I am looking for hard-masked hs37d5 reference. Does anybody know where I can get it? Any help is appreciated.

ADD REPLY • link 3.4 years ago by AshNY • 0

score 0 · Answer 1 · 2013-08-07

you could use the chromosomes of the UCSC :

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/

This directory contains the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))

chr*.fa.gz: compressed FASTA sequence of each chromosome.

(...)

Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.