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Gff Or Bed File For Hg19 Genome

Could some one point me to a URL to download the gff/ gtf/ bed reference file for hg19 which i want to use to map whole genome DNA seq file

Thanks

genome seq gff hg19
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updated by h.mon h.mon • written by rob.costa1234 rob.costa1234

2 answers

Just use the UCSC table browser.

• 1,110 views • link
written by Devon Ryan Devon Ryan

if you have a fasta file such as then human reference

human_hg19.fa

and you samtools index it

samtools faidx human_hg19.fa

then you can generate the whole genome bed file by entering, using awk for instance, a "0" column between the first 2 columns of the .fai file generated previously

awk '{print $1 "\t0\t" $2}' human_hg19.fa.fai > human_hg19.bed
• 0 views • link
written by Jorge Amigo Jorge Amigo

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