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ashkot 04-03-2012 04:24 PM

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.

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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