How To Get The Sequence Of A Genomic Region From Ucsc?

Question: How To Get The Sequence Of A Genomic Region From Ucsc?

9.9 years ago by

London, UK

Let's say I want to download the fasta sequence of the region chr1:100000..200000 from the UCSC browser. How do you do that? I can't find a button to 'export to fasta' in the UCSC genome browser. I think that the solution is to click on one of the tracks displayed, but I am not sure of which. If I go to the Tables section, I can't find a table with the fasta sequences among the many.

fasta sequence ucsc • 68k views

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modified 3.6 years ago by jayanthisreejith7 • 10 • written 9.9 years ago by Giovanni M Dall'Olio ♦ 26k

9.9 years ago by

Pierre Lindenbaum ♦ 125k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 125k wrote:

Use the DAS server:

http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr1:100000,200000

ADD COMMENT • link modified 7.4 years ago by Istvan Albert ♦♦ 82k • written 9.9 years ago by Pierre Lindenbaum ♦ 125k

be careful: the DAS server uses an index of (+1) for the first base.

ADD REPLY • link written 9.9 years ago by Pierre Lindenbaum ♦ 125k

that's really neat!

ADD REPLY • link written 9.9 years ago by Istvan Albert ♦♦ 82k

Thanks!! I didn't know that, very cool!! :-)

ADD REPLY • link written 9.9 years ago by Giovanni M Dall'Olio ♦ 26k

Wow, thanks. That's quite useful.

ADD REPLY • link written 9.9 years ago by Madelaine Gogol ♦ 5.1k

9.9 years ago by

Madelaine Gogol ♦ 5.1k

Kansas City

Madelaine Gogol ♦ 5.1k wrote:

Just click "DNA" at the top of the screen.

ADD COMMENT • link written 9.9 years ago by Madelaine Gogol ♦ 5.1k

Currently, you need to go to "View --> DNA," but the function is the same

ADD REPLY • link written 5.7 years ago by Charles Warden ♦ 7.5k

5.9 years ago by

Maximilian Haeussler • 1.3k

UCSC

Maximilian Haeussler • 1.3k wrote:

There is no table with sequences. The sequences are in a file because that's a lot faster.

I think the question was mostly about how to get a single sequence and the answer to that is very simple: click View - DNA.

If you need to get the sequence from a script, use the UCSC utility twoBitToFa (see http://hgdownload.cse.ucsc.edu/admin/exe/) like this:

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa
chmod a+x twoBitToFa
twoBitToFa http://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit test.fa -seq=chr21 -start=1 -end=10000

ADD COMMENT • link modified 21 months ago • written 5.9 years ago by Maximilian Haeussler • 1.3k

This is exactly what I was looking for Thanks!!!

ADD REPLY • link written 5.9 years ago by vivekdna • 0

5.3 years ago by

Hiroyuki Mishima • 140

Nagasaki. Japan

Hiroyuki Mishima • 140 wrote:

Yet another solution.

TogoWS's REST API now supports the UCSC Genome Database.

For example, http://togows.org/api/ucsc/hg38/chr1:12,345-12,500.fasta returns the reference genome sequence in the fasta format.

Please see further information at the "External API" section of http://togows.org/help/

ADD COMMENT • link written 5.3 years ago by Hiroyuki Mishima • 140

9.9 years ago by

Istvan Albert ♦♦ 82k

University Park, USA

Istvan Albert ♦♦ 82k wrote:

The Genome Browser is for visualization.

To get data in many formats use the UCSC Table Browser then select the output format of your choice.

You may also need to select the right group and track to get the data you want.

ADD COMMENT • link written 9.9 years ago by Istvan Albert ♦♦ 82k

I tought so, but I can't find the table for sequences, not even when I select 'All tracks' and 'AlLl tables'. Thanks anyway..

ADD REPLY • link written 9.9 years ago by Giovanni M Dall'Olio ♦ 26k

I guess you are right, now that I tried myself and it seems that information is awfully hard to get - sometimes the seemingly getting the easiest thing is not possible. You could try your luck with the Ensemble API.

ADD REPLY • link written 9.9 years ago by Istvan Albert ♦♦ 82k

I guess you are right, now that I tried myself and it seems that information is awfully hard to get - sometimes getting something seemingly easy end up as being not possible. You could try your luck with the Ensemble API.

ADD REPLY • link written 9.9 years ago by Istvan Albert ♦♦ 82k

I you need to download sequences, first you need to tell the website the coordinates that you want to download. (Remember that table browser is for batch processing). Click on "Custom track" and type in something like this:

chr1 1 1000
chr2 123 12345

Click Submit.

Now you can go to the table browser, select your "custom track" and select "Fasta format" as output format.

The advantage of this procedure is that you can request thousands of sequences in one go. No need to use an API. For scripting see my reply above that uses the linux command line tool "twoBitToFa" from UCSC.

ADD REPLY • link modified 4.6 years ago • written 5.5 years ago by Maximilian Haeussler • 1.3k

I think, now UCSC browser has changed. Even I have the same query, but unable to fetch FASTA sequence using the coordinates. Can u explain using the given link.. https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=703655381_NWHqxkgVDaPPscUhaKxyA9bAbb7e

ADD REPLY • link modified 13 months ago • written 13 months ago by shuksi1984 • 50

4.2 years ago by

pengchy • 410

China/Beijing

pengchy • 410 wrote:

Another solution is using Heng Li's sequence toolkit:

seqtk subseq

Usage:   seqtk subseq [options] <in.fa> <in.bed>|<name.list>

Options: -t       TAB delimited output
         -l INT   sequence line length [0]

Note: Use 'samtools faidx' if only a few regions are intended.

which can be downloaded from: https://github.com/lh3/seqtk , however, seqtk subseq does not consider the strand information, which has been implemented in bedtools getfasta

bedtools getfasta

Tool:    bedtools getfasta (aka fastaFromBed)
Version: v2.23.0
Summary: Extract DNA sequences into a fasta file based on feature coordinates.

Usage:   bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> 

Options: 
        -fi     Input FASTA file
        -bed    BED/GFF/VCF file of ranges to extract from -fi
        -fo     Output file (can be FASTA or TAB-delimited)
        -name   Use the name field for the FASTA header
        -split  given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons)
        -tab    Write output in TAB delimited format.
                - Default is FASTA format.

        -s      Force strandedness. If the feature occupies the antisense,
                strand, the sequence will be reverse complemented.
                - By default, strand information is ignored.

        -fullHeader     Use full fasta header.
                - By default, only the word before the first space or tab is used.

ADD COMMENT • link modified 4.2 years ago • written 4.2 years ago by pengchy • 410

Thanks, this is really handy!!

ADD REPLY • link written 2.3 years ago by phosphodiester_bond • 30

3.6 years ago by

jayanthisreejith7 • 10

jayanthisreejith7 • 10 wrote:

I understand this is a very old post, but if it helps anyone who is searching for programmatic access directly using UCSC tools, I found the below link http://genomewiki.ucsc.edu/index.php/Programmatic_access_to_the_Genome_Browser

It has details on

1) How to download data from their MySQL database

2) Get Chromosome sequence for a range (using REST API, which was what I was looking for)

... and few such things including accessing a copy of current Genome browser image

Hope this helps!

ADD COMMENT • link written 3.6 years ago by jayanthisreejith7 • 10

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