Dana Wyman
Dana Wyman
Hi, When you initialize a TALON database with a blank GTF, you essentially get an empty database, which leads to problems downstream as you noticed because no genome build or...
Hi Arun, I'd be happy to take a look. You can send the GTF to me at [email protected]. Best, Dana
Thank you, I will keep that in mind for a future version. The X may pose a slight challenge because there is an internal step that merges the MD tag...
No problem- a note has been added to the README. I will work on the compatibility issue.
When I initially developed the code, the PacBio reads I was using lacked a quality score altogether, so it wasn't something I thought a lot about. This seems like it...
Hi Matt, Have you tried running the TranscriptClean 2.0 version on this data instead of the patch update? I am hopeful that my test cases covered this issue in the...
Update: I was able to find an example in some data I had of a noisy read that triggered a possibly related problem during non canonical splice junction correction. I...
Hi Matt, Thank you for bringing this to my attention. I will take a look at the files you sent and see if I can reproduce the issue. Best, Dana
Hi Matt, So I tried to reproduce the issue with the latest TranscriptClean version (including reducing it down to a small test case of one junction), and I have not...
Hi Dean, I'll try the trivial solution first- have you double-checked that the path you are providing in the $SSAM bash variable is correct? If that doesn't help, feel free...