Yarden Katz
Yarden Katz
@sepidehparhami we need better error handling here for sure. The bigger issue is that there isn't a general way to parse the output of each cluster submission system to tell...
I believe this is already fixed in the github version but will be incorporated into next release.
There's a simpler way to do this. All you'd need is a wrapper script like send_job that takes a shell script as input and submits it to the cluster, passing...
There are efficient ways to calculate insert size distribution and many tools that do it apart from MISO (though I don't have experience with them myself). Our code for calculating...
Hi Rory, Thanks -- yes, definitely, we're working on this actively and plan to add support for biological replicates soon. We're playing with a few principled approaches to pooling and...
Hi all, Thanks for reporting this. Perhaps I'm misunderstanding - the docs for shelve say multiple reads are fine ("Multiple simultaneous read accesses are safe"), from here: https://docs.python.org/2/library/shelve.html and I...
To clarify, this is different jobs -- i.e. distinct jobs on a cluster, right? What was the error that you got?
Hi Olga, Thanks for this nice test case - I just reproduced it. It's most certainly a bug. I'm looking into it now.
Hi Olga, It appears that the read length is 92 and your short isoform is 90, less than the read length, and this is what caused it.
I agree it's not intuitive, but here's one explanation. Since your read length is 92 and the shortest isoform is 90, it's not possible -- unless you consider non-end-to-end alignments,...