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  • 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.

  • #2
    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).

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    • #3
      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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