Query Ensemble or USCS

[ashkot]

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]

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]

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.