People I work for love the juncBASE output, but I've been having major issues with the software:
- I have only gotten it to work to display the correct genes when I use UCSC mapping, etc. (which has 'chr' prefix) but not with Ensembl. When I use Ensembl most events are considered N (novel) rather than K (known), and some genes listed are clearly wrong with wrong chr, etc.
- There are thread/process issues so that some of the samples never complete. Worst, the last samples listed sometimes are shown to have completed but have different results than if they were run somewhere in the middle of the command. I suspect this problem is due to thread/process issues with the last 2 samples.
- I could deal with 2. above by running it, saving the results and then swapping the last samples with some in the middle of the command and rerunning to get the correct results for the last 2 samples, but sometimes even samples listed in the middle have different results each time juncBASE is run.
I have tried to contact the author, but usually these conversations take months of back and forth and nothing ever gets resolved. I was wondering if anyone else has run into these issues and has any insight into the matter?
I tried to use MATS instead but my customers didn't like the output.
I'm seriously considering writing a new software as this one seems unusable?
I'd love to hear from you about this matter.