Mapping genome region to gene symbols in CNV files from TCGA
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
2 answers
- Get the RefSeq Gene co-ordinate from UCSC Table Browser (output in bed format)
- Convert your input coordinates (from TCGA CNV Level-3) into bed format
- 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
Here you go: Find Out The Genes That Correspond To My Coordinates
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