Question: Where can I download hg18.fa that includes all chromosomes?
0
gravatar for allyson1115ar
2.8 years ago by
allyson1115ar20 wrote:

In UCSC genome browser, the hg18 provided is not in one fasta file. They provide file to download for each chromosomes. May I know where can I download a hg18 complete fasta file that include all chromosomes? Thanks.

chromosome hg18 fasta genome • 1.8k views
ADD COMMENTlink modified 2.8 years ago by Selenocysteine550 • written 2.8 years ago by allyson1115ar20
0
gravatar for Selenocysteine
2.8 years ago by
Dublin, Ireland
Selenocysteine550 wrote:

http://hgdownload.cse.ucsc.edu/downloads.html

Here, scroll down until you reach hg18 and then full dataset.

ADD COMMENTlink written 2.8 years ago by Selenocysteine550

After I clicked 'full dataset', the only way for me to get hg18.fa is by downloading hg18.2bit and use twoBitToFa to convert to hg18.fa right? is there any link allow me to straight away download the hg18.fa without doing the conversion from twoBitToFa? thanks for your advice

ADD REPLYlink written 2.8 years ago by allyson1115ar20

Download the fasta files for each chromosome and use cat to concatenate them. Alternatively, find out the last Ensembl release to use hg18 and download that fasta file.

ADD REPLYlink written 2.8 years ago by Devon Ryan88k

This should give you full hg18 in one file from UCSC.

ADD REPLYlink written 2.8 years ago by genomax63k

The readme suggests that that's one file per-chromosome. I get the feeling that the multifasta file didn't become standard at UCSC until sometime after 2006.

ADD REPLYlink written 2.8 years ago by Devon Ryan88k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1916 users visited in the last hour