Question: Gff Or Bed File For Hg19 Genome
0
gravatar for rob.costa1234
6.1 years ago by
rob.costa1234180
United States
rob.costa1234180 wrote:

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

hg19 gff seq genome • 13k views
ADD COMMENTlink modified 16 months ago by h.mon27k • written 6.1 years ago by rob.costa1234180
4
gravatar for Devon Ryan
6.1 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Just use the UCSC table browser.

ADD COMMENTlink written 6.1 years ago by Devon Ryan92k
3
gravatar for Jorge Amigo
3.7 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Jorge Amigo11k
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