Mapping genome region to gene symbols in CNV files from TCGA

Question

[Na Sed]

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

Answer 1

[raunakms]

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

Answer 2

[Deepak Tanwar]

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