Gff Or Bed File For Hg19 Genome

Question

[rob.costa1234]

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

Answer 1

[Devon Ryan]

Just use the UCSC table browser.

Answer 2

[Jorge Amigo]

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