Delaney Sullivan

It is an autoconf issue; installing the newest version of htslib will not fix the issue (kallisto comes bundled with an older version of htslib, not htslib 1.12). You need...

It won't work. Kallisto relies on the older version of htslib and I think there are updates in the newer version of htslib that make it incompatible with kallisto. One...

Yes, it is suitable for 5' chemistry and should be no different than 10X v2 chemistry (i.e. your first fastq file contains your 16bp barcode and 10bp UMI and your...

Thanks for the follow up clarification. I see you've tried a few things here: https://github.com/pachterlab/kallisto/issues/226#issuecomment-931297217 (issue #226 ) You can indeed specify multiple sequences in the technology string, however, you...

^kallisto runs on windows and through RStudio, but the issue is probably the &> at the end of the command. I can't really fix this on the kallisto end as...

^It works on the Mac command-line terminal. Not sure about RStudio though (I don't usually run things on it)

Yes, you can try sleuth for differential expression. For help with tximport, that's not our package. Post your tximport questions on the bioconductor support forum.

Thanks for letting me know. I'm a bit busy right now but will put it on my to-do list. I'm meeting with Harold Pimentel (the first author of the original...

Can you show us the exact command you're running and the error message?

It should be in the technologies list (BDWTA). Perhaps update your version of kb