Rob Patro

Hi @reganhayward, Thank you for the detailed report. It's interesting that this happens when running with STAR but not when running with selective alignment. However, salmon will attempt to solve...

Thanks @reganhayward. I'm pinging @hiraksarkar here as well as he can help us dig into this. I do think it will be really useful to have the bootstrap (in this...

Hi @hiraksarkar , The results @reganhayward included above are with `-d`, so we have the equivalence classes. The gibbs samples were big, so not included, but I’ve asked him to...

Thanks @tamuanand for the (as always) detailed and clear question! Since this directly involves `tximport` and `DESeq2` downstream, let me also ping @mikelove here.

Thanks for the detailed report @idinsmore1, These are quite different versions of ensembl, and so changes in the underlying transcriptome can absolutely have an effect on estimated abundances. Specifically, as...

It may be a bad alloc error. Do you have a machine with a bit more ram to try it on? Also, you could try installing through bioconda to see...

We do no have access to BSD-based systems (apart from the extent to which OSX can be said to be BSD-based) on which to test during development. Bioconda works on...

Hi @klentaq , Thank you for the detailed report; it's much appreciated. I'll dig into this more as soon as i get back in front of a computer, and report...

Hi @rahulnutron, Currently, the recommendation is to move to [`alevin-fry`](https://github.com/COMBINE-lab/alevin-fry). If you don't have a good annotation (i.e. transcripts as well as introns) then you can index just the transcriptome...

Hi @sjroth, This is strange. I'll ping @k3yavi here to see if he has any thoughts about what might be going on.