Warren McGee

pinging @pmelsted @pimentel: We have a user here and on the [google group](https://groups.google.com/forum/#!topic/kallisto-sleuth-users/pDh2Cy551Ew) both reporting odd behavior with the % of reads pseudoaligned when handling paired-end data. Is this a...

Hi @leagleag, It appears that your calculations are correct. Thanks for the update! I forgot to ask a critical question of you and @chrarnold: what was the protocol for preparing...

Hi @teshomem, It appears that there is an error that occurs during the summarizing step, and it's happening in all cores (`2: In parallel::mclapply(x, y, mc.cores = num_cores) : all...

Hi @teshomem, If all scheduled cores encountered errors, the script should break on your first sample and should be done pretty quickly. If it doesn't, then there might be issues...

Hi @teshomem, Your link doesn't work. Has at least one sample been processed? It would be odd for it be stuck after all this time on just one sample.

I tried the link [http://dpaste.com/386YKWB](http://dpaste.com/386YKWB), and I got your file. For future reference, you can directly post a file onto GitHub using these instructions: [link](https://help.github.com/articles/file-attachments-on-issues-and-pull-requests/). A few questions: 1) Is...

Ah, I see. The dots are the way to keep track of how many samples have been processed. So, before you killed the job, it had processed what looks like...

Hi @teshomem, I'm glad your problem was solved. I'm changing the name of this issue to reflect the real remaining problem, which is requesting the improvements you've mentioned. Pinging @pimentel...

@pimentel, it appears that updated documentation for `sleuth_prep` has not made it to the sleuth website, as mentioned in a comment with #120. Since that is a separate script from...

If you updated to the latest `devel` branch, the ability to do gene-level aggregation of counts is currently turned off for reasons of other things that are being implemented, and...