Question: how to get Homo_sapiens.GRCh38.84.bed file
1
gravatar for yuxinghai
18 months ago by
yuxinghai10
yuxinghai10 wrote:

I'm using geneBody_coverage2.py in RseQC package to calculate Read coverage over gene body, which need a bed12 file. I did alignment based on Homo_sapiens.GRCh38.84.gtf , so i need a Homo_sapiens.GRCh38.84.bed. But gtfToBed can't produce a BED12 file, how can I get it? anyone can help me?

annotiation rna-seq gene • 889 views
ADD COMMENTlink modified 18 months ago by Devon Ryan82k • written 18 months ago by yuxinghai10
8
gravatar for Devon Ryan
18 months ago by
Devon Ryan82k
Freiburg, Germany
Devon Ryan82k wrote:

awk '{if($3 != "gene") print $0}' Homo_sapiens.GRCh38.84.gtf | grep -v "^#" | gtfToGenePred /dev/stdin /dev/stdout | genePredToBed stdin Homo_sapiens.GRCh38.84.bed

You can download the two tools from UCSC.

If you're curious, this is from here and is essentially the code I use to generate the reference data for our institute.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Devon Ryan82k
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