Hello, Lan.
If you have sequence, but no coordinates, it sounds like you need to use our
BLAT utility, located at http://genome.ucsc.edu/cgi-bin/hgBlat. You can
paste your sequence into the text box or upload a file containing the
sequences. Simply set Genome/Assembly to Human/hg19, set the remaining
options to the settings of your choice and click the "submit" button.
Note that the web-based BLAT utility is limited to 25 sequences per query.
If you have a higher volume of sequences you need to BLAT, there is also a
command line utility that can be downloaded from
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: genome-***@soe.ucsc.edu [mailto:genome-***@soe.ucsc.edu] On
Behalf Of Ko, Lan
Sent: Wednesday, June 27, 2012 9:10 AM
To: ***@soe.ucsc.edu
Subject: Re: [Genome] hg19
Dear Steve:
This is exactly why I can only get FASTA sequence but not hg19 sequence. I
have sequence, but how can I print it out with hg19 coordinates next to it?
Many thanks,
Lan Ko
-----Original Message-----
From: Steve Heitner [mailto:***@soe.ucsc.edu]
Sent: Tuesday, June 26, 2012 7:16 PM
To: Ko, Lan; ***@soe.ucsc.edu
Subject: RE: [Genome] hg19
Hello, Lan.
If you have a list of genomic coordinates, you can use our Table Browser to
obtain the sequences. If you're unfamiliar with the Table Browser, please
see the User's Guide at
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
To obtain the sequences, perform the following steps:
1. Go to http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: knownGene
Region: Click the "define regions" button to paste or upload your list of
coordinates Output format: sequence Output file: Leave this blank to view
the results on the screen, otherwise enter a filename to save your results
to a file
3. Click the "get output" button
4. Select "genomic" and click the "submit" button
5. Select your desired options and click the "get sequence" button
Please contact us again at ***@soe.ucsc.edu if you have any further
questions.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: genome-***@soe.ucsc.edu [mailto:genome-***@soe.ucsc.edu] On
Behalf Of Ko, Lan
Sent: Tuesday, June 26, 2012 3:15 PM
To: ***@soe.ucsc.edu
Subject: [Genome] hg19
Dear UCSC:
I need to get a gene sequence with hg19 coordinates but not FASTA format.
How should I download from your browser?
Thank you.
Lan Ko
_______________________________________________
Genome maillist - ***@soe.ucsc.edu
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - ***@soe.ucsc.edu
https://lists.soe.ucsc.edu/mailman/listinfo/genome