adding Gene Name to my bed file

Question

[manojkumarbioinfo]

Hi,

I have a bed file i would like to add gene name to my bedfile.

My bed file

chr1    11167489    11167609
chr1    11168230    11168350
chr1    11169327    11169447
chr1    11169686    11169806
chr1    11172881    11173001
chr1    11174331    11174571

[Carlo Yague]

Please see add gene names in bed file

[Alex Reynolds]

What assembly are you using?

[manojkumarbioinfo]

im using hg 38

Answer 1

[manojkumarbioinfo]

I used CNVkit to add gene name to my bedfile

cnvkit.py target your.bed --annotate your_refFlat.txt -o output.bed

GRCH38 ref_Flat file can be downloaded http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/

HG19/GRCH37 ref_Flat file can be downloaded https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/