Mike Axtell

Link https://www.dropbox.com/s/eqx3jmylgns4wd3/Trapnell_results.zip?dl=1 is still a 404 not found From: Fronttooth Reply-To: pachterlab/sleuth Date: Friday, September 13, 2019 at 7:23 AM To: pachterlab/sleuth Cc: "Axtell, Michael" , Author Subject: Re: [pachterlab/sleuth]...

This looks straightforward, thank you. But I would like to first see an example where the div by 0 error appears. I've never seen that happen in any of my...

Yeah, umm, sorry for not responding for over a year ! I will run this down in the next major release, which I have begun working on.

ShortStack version 4 is now available for alpha testing on the ShortStack4 branch. It will be merged into master and released once we complete testing. But it should solve this...

Thanks Cei, sorry to be so slow to respond. I am working through all of the open issues now, finally. I have begun work on a major new release and...

A large upgrade of ShortStack, version 4, is now in alpha testing. It is available if you want to test it on the ShortStack4 branch on GitHub. We are still...

Hi Bernadette, thanks for your question! I think this is about what I would expect. Differential expression is a completely different protocol compared to ShortStack's cluster definition methods. Differential expression...

Hello Stefano, Sorry for slow response. Just back from vacation. ‘.’ strand is a valid entry in GFF3 format and denoted unstranded features. When it appears in a ShortStack-generated annotation...

The Results.txt file has a column called 'FracTop' which lists the fraction of alignments mapped to the + genomic strand. This will be a float between 0 and 1. You...

Thanks to Bojan Losic for pointing this out.