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.