Rob Patro

Tagging @k3yavi on this one!

Hi @k3yavi and @AnnaAMonaco, There was some workflow I recall reading that extracted intervals from the genome (bins) and then essentially treated these as transcripts. It seemed like it might...

Hi @SeBaBInf, Thanks for reporting this. I'm pinging @k3yavi for his thoughts here. Two quick thoughts though -- the first is that the abstract for this paper mentions 5' tagged...

@ctb, This seems to explain the source of the issue : https://twitter.com/dpryan79/status/1368116490801717251?s=19. It looks like it will be fixed upstream (hopefully soon). --Rob

Hi @hsi88, It looks like there was an allocation error while reading the input. This exception terminated the program (which resulted in the FastxParser destructor error happening simultaneously in a...

Hi @uros-sipetic, Yup; these are both good ideas. The `quantmerge` command was added mainly for convenience for a use case @tseemann was interested in. However, given that it's now part...

Hi @kate-simonova, How low is your mapping rate? Can you explicitly pass the flag `-l IU` for library type? This strand bias means that the data look stranded however. Also,...

Hi @kate-simonova, While I would certainly recommend updating to the latest version of salmon (which, given the pre 1.0.0 to post 1.0.0 difference would require you to rebuild the index),...

The assumptions made by salmon regarding the BAM files are the same as those made by RSEM (with the exception that salmon will accept alignments with insertions or deletions in...

Hi scott, Thank you for the detailed report. Im trying to reproduce the issue. So far, i have been unable to reproduce the issue on an ubuntu 16.04 or OSX...