Query Ensemble or USCS

ashkot · 04-03-2012, 04:24 PM

Is there any automated way to get DNA sequences from UCSC genome browser or Ensemble for a list of chromosomal coordinates of interest.

I have several chromosomal coordinates sets and cannot do it manually.

Thanks in advance.

dpryan · 04-04-2012, 03:28 AM

If you have a bunch of ranges, then it might be most straight forward to just download the genomes in fasta format and just write a quick parser (samtools provides an fai_fetch function in the C API that can be given a genomic range and will return the sequence).

mgogol · 04-04-2012, 06:30 AM

At UCSC, you can upload a custom track bed file, then use the table browser and do an intersection. You could also do this with galaxy "Fetch Sequences".

On the command line, you have a number of options... bedtools getfasta comes to mind.

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04-03-2012, 04:24 PM	#1
ashkot Member Location: Cupertino, CA Join Date: Nov 2011 Posts: 59	Query Ensemble or USCS Is there any automated way to get DNA sequences from UCSC genome browser or Ensemble for a list of chromosomal coordinates of interest. I have several chromosomal coordinates sets and cannot do it manually. Thanks in advance.

04-04-2012, 03:28 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	If you have a bunch of ranges, then it might be most straight forward to just download the genomes in fasta format and just write a quick parser (samtools provides an fai_fetch function in the C API that can be given a genomic range and will return the sequence).

04-04-2012, 06:30 AM	#3
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	At UCSC, you can upload a custom track bed file, then use the table browser and do an intersection. You could also do this with galaxy "Fetch Sequences". On the command line, you have a number of options... bedtools getfasta comes to mind.