Hi,

I aligned both my transcriptome and reads to genome and found reads have been aligned outside the transcript boundaries. For an example, if a transcript "X" ranges from 5670 to 6540, there are lot of reads that have aligned upstream of 5670.

Now I would like incorporate those reads also. If there are reads aligned from position 5432 and overlaps till 5673, then I would like to get an output of 5432 to 5673 in bed format(or any other readable format). In short, I would like identify the regions outside my transcript boundaries which has coverage and would like to extend my transcript boundaries.

Any guidance would be really grateful