Closed:Generate BED12 file from genomic coordinates

Question

[Barry Digby]

Hi all,

As the title suggests, is it possible to generate a bed12 file given a genomic range?

Here are some examples;

Standard bed file:

chr22   20564449    20566817    circrna 0   +

I would like to generate a bed12 file from the underlying sequence that would ultimately result in:

chr22   20564449    20566817    circrna 0   +   20564449    20564449    0,0,0   2   239,351 0,2017

Red: genomic range, Blue: GTF, Black: desired bed12 output

I have also considered if the genomic range is intronic, in which case the sequence is represented as 1 exon block:

---

The goal here is to use bedtools getfasta with the -split flag to retrieve the concatenated exon sequences / intron sequence.

Thanks,

Barry