Question: bed file of gene body fro hg19
0
gravatar for kanwarjag
4.9 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

Can some one direct me where can I find gene body coordinates as bed file (other format) for Hg19. I want to use it in IGV

hg19 gene body • 2.0k views
ADD COMMENTlink modified 4.9 years ago by Alex Reynolds29k • written 4.9 years ago by kanwarjag1.0k
1
gravatar for Alex Reynolds
4.9 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

One way via the command line:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/release_21/gencode.21.annotation.gtf.gz \
    | gunzip --stdout - \
    | gtf2bed - \
    > gencode.21.bed​
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Alex Reynolds29k

Just a clarification: Gencode 21 is GRCh38 :

Gencode 19  supports GRCH37 (~/hg19/) http://www.gencodegenes.org/releases/

ADD REPLYlink written 4.8 years ago by Rm7.9k
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