How can I retrieve genomic sequences from ENSEMBL in a window both up stream and downstream of the TSS?

Question

[daniel.zhang]

Is there a way to use bioMART on the ensemble.org website to retrieve genomic sequences in a window (ie. 500 bp) both upstream and downstream of the annotated TSS for selected genes? So far, I can only retrieve genomic sequences either upstream or downstream, but not both.

Answer 1

[boczniak767]

Do you really need biomart? If not you can download gff with gene information, extract only genes to bed with TSS coordinate for both start and end (2nd and 3rd columns) with awk and use samtools slop to retrieve requested range. Retrieval of TSS to bed should be done for each strand separately.

As you see it requires some coding. Maybe somebody else can provide simpler solution.

Answer 2

[Emily]

You could use the Ensembl REST API. Use one of the Lookup endpoints to get the TSS of the gene (check the strand, if the gene is +, TSS is the start, if it's -, TSS is the end). Then use that with the sequence region endpoint to get that sequence with the expand options. You can copy most of the code from exercise 5.2 of this online course but just switch to the sequence endpoint.