I had downloaded TCGA CNV level 3 data(nocnv, hg19). I hope to map this CNV data to each genes. So, I had searched information about this issue and I could find some.
I got recommendation, using the bedtools.
I had downloaded refseq file from UCSC table browser. refseq file's content is as follows.
bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts
3 NR_130130 chr1 + 150980866 151008189 151008189 151008189 4 150980866,150997990,150999708,151006281,
3 NR_130132 chr1 + 150980866 151008189 151008189 151008189 4 150980866,150990287,150999708,151006281,
and cnv seg file's content is as follows.
Sample Chromosome Start End Num_Probes Segment_Mean BREAD_p_TCGAb_430_431_NSP_GenomeWideSNP_6_D11_1538030 1 3218610 247813706 128998 0.0014 BREAD_p_TCGAb_430_431_NSP_GenomeWideSNP_6_D11_1538030 2 484222 207696262 110158 0.0067 BREAD_p_TCGAb_430_431_NSP_GenomeWideSNP_6_D11_1538030 2 207696273 207701151 2 -1.5215
As far as I know, I have to convert to my files(cnv seg, refseq) to .bed format. But I don't know how to deal it. What should I do?
Can you give me a hand?