Open schelhorn opened 8 years ago
Sorry to bother, but would anyone be able to answer this question? Thank you.
It appears that the software is no longer being maintained. There haven't been any bug fixes in almost a year, nor any replies to Issues tracker, either.
I'm sticking with STAR for now.
How about heading over to Salmon? The Salmon developers are extremely responsive.
You can see lots of active discussions here: https://github.com/COMBINE-lab/salmon/issues
Hi @schelhorn, sorry for the late reply. We are working on fusion calling directly in kallisto and will be releasing the code in the coming weeks.
As far as bug fixes go, most of them have been addressed and will go into the next release. The lastest one fixed was upstream in the kseq library https://github.com/attractivechaos/klib/issues/78
Excellent news, thank you. Will kallisto stick with the closed commercial license, or will you open that up at some point? I'd love to use you tool for pharma research, but I don't see us purchasing a license for it anytime soon.
@schelhorn Kallisto is free for academics research as long as you're not making money. You don't need to ask. https://github.com/pachterlab/kallisto/blob/master/license.txt
So, things have changed. Lior has changed the license, and very gracefully. And you guys have made and released pizzly. Thanks for both.
Hello @lakigigar and co-developers,
we're currently running @chapmanb's bcbio in production for quantitating RNA-Seq expression and calling gene fusion events; thanks to @roryk's work bcbio supports the triad of
hisat2
,salmon
, andkallisto
for the former (to different degrees), andstar
in combination withoncofuse
for the latter.The issue with
star
, while being a great approach in itself, is it's huge appetite for memory due to the reliance on full genomic alignments, as well as its incompatibility withhg38
, a fact that does not seem to change anytime soon. We would therefore like to have a look at the newer three approaches for both expression quantitation and RNA-Seq gene fusion calling. Unfortunately, none ofhisat2
,salmon
, andkallisto
seem to support calling gene fusions explicitly at the moment. While some of these methods support generating BAM files with pseudo-alignments that may be usable by dedicated gene fusion calling pipelines, no such approach has been documented where it can be found easily (i.e., by googling the relevant terms).To accelerate usage of fast hg38 gene fusion pipelines we would be willing to spend developer time on integrating an existing approach into bcbio. In order to better determine which approach to use I have already raised the issue with
salmon
(discussion), andhisat2
(discussion) to get the conversation going.kallisto
seems to support gene fusion calling as well, but evidence is anecdotal. May I ask you to elaborate on your view of the issue, both in general and specifically as regardskallisto
?