Whippet.jl
Whippet.jl copied to clipboard
timbitz
Lightweight and Fast; RNA-seq quantification at the event-level
Hello, I've been trying out whippet v0.11 with some stranded RNA-seq data and obtained a weird result. With whippet_quant.jl and `--stranded` I get only a small % of reads mapping...
This PR changes the default of `whippet-delta.jl` to a read-depth independent method of differential splicing. The current default is still available using the optional command line flag `--use-depth`.
- [ ] Re-implement threaded.jl for multithreading performance Moved from #29
It would be nice to integrate a visualization tool like sashimi plots or write a fast version
This seems like it should improve the accuracy of K1 events. However the current implementation in the `mappability` branch actually slightly decreases, rather than improves accuracy.
This seems to be a necessary feature for those who would rather substitute a little performance for more exhaustive mappability. A multiseed 'stitching' implementation should overcome the major caveat of...
There has been a substantial interest in a Whippet feature to use all edges to produce full isoforms. - [x] Alter annotation support to load all known edges. - [...
This is could go either way, for now it is on hold. @weatheritt2 any preferences?
This is moved from #14
Hello, I ran Whippet on two different datasets with the same annotation index but I don't have the same number of events or exons (CE) in the psi files. I'm...
