If one tries to use --output-mode=segments together with the --use-strand switch, to get transcript sequences from bed12 files, the output is incorrect for negative strand transcripts. The sequences of the indevidual exons are corrects reverse complemented, but then they are concatenated in the wrong order.
I will try to fix this if I get time, shouldn't be hard, I'm just busy.
If one tries to use
--output-mode=segmentstogether with the--use-strandswitch, to get transcript sequences from bed12 files, the output is incorrect for negative strand transcripts. The sequences of the indevidual exons are corrects reverse complemented, but then they are concatenated in the wrong order.I will try to fix this if I get time, shouldn't be hard, I'm just busy.