We are trying to use RSeQC with our RNA Seq samples. I have tried using several BED files (the hg19 one provided, the RefSeq and UCSC BED files downloaded from the folder on source forge) but none of them seem to be working.
When I use the 'junction_annotation.py' module, my output shows that 100% of the transcripts assembled are novel which is not true. I am not sure what is going on and why this is the case ? Any help/thoughts on this would be highly appreciated.
Hi,
We are trying to use RSeQC with our RNA Seq samples. I have tried using several BED files (the hg19 one provided, the RefSeq and UCSC BED files downloaded from the folder on source forge) but none of them seem to be working.
When I use the 'junction_annotation.py' module, my output shows that 100% of the transcripts assembled are novel which is not true. I am not sure what is going on and why this is the case ? Any help/thoughts on this would be highly appreciated.
Thank you.
Aditi Kulkarni
Last edit: Aditi Kulkarni 2018-07-11