adding Gene Name to my bed file
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12 months ago

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
name annotation gene bed • 680 views
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What assembly are you using?

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im using hg 38

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9 months ago

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/

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