Question: Mapping genome region to gene symbols in CNV files from TCGA
2
gravatar for Na Sed
4.1 years ago by
Na Sed280
United States
Na Sed280 wrote:

I have just downloaded CNV level 3 files from TCGA database.

As you know, in these files there are three columns: chromosome, start, and end which presents the coordinates of genes.

Now, I would like to map them to gene symbols, but I don't know.

I appreciate any help.

Thanks

cnv genome region R gene symbols • 3.4k views
ADD COMMENTlink modified 4.1 years ago by raunakms1.1k • written 4.1 years ago by Na Sed280
8
gravatar for raunakms
4.1 years ago by
raunakms1.1k
Vancouver, BC, Canada
raunakms1.1k wrote:
  1. Get the RefSeq Gene co-ordinate from UCSC Table Browser (output in bed format)
  2. Convert your input coordinates (from TCGA CNV Level-3) into bed format
  3. Use BEDTools, command: intersectbed to match two bed files. This will give you a list of cnv segments and the matched RefSeq Genes.

For Example: (refer to the documentations of BEDTools for the usage of -wa -wb)

intersectBed -a file_cnv_seg.bed -b file_ucsc_refseq.bed -wa -wb > file_output.bed

 

ADD COMMENTlink written 4.1 years ago by raunakms1.1k
4
gravatar for Deepak Tanwar
4.1 years ago by
Deepak Tanwar3.9k
ETH Zürich, Switzerland
Deepak Tanwar3.9k wrote:

Here you go: Find Out The Genes That Correspond To My Coordinates

ADD COMMENTlink written 4.1 years ago by Deepak Tanwar3.9k
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