John Urban

tombo access to tarballs to offset issues of file and storage limits

6

Hi Marcus, I didn't look at all the code to be sure -- but it seems like accessing tarballs is not an option for Tombo (given a skimming of the...

h5py unable to open object

10

Opened by Jean-Michel Carter. Dear John, I have been using your poreminion program but it has recently started giving me errors that seem to be related to h5py. I am...

marginStats

2

Hi, Thanks for the marginAlign suite. It is great. I was wondering if there was a way to have marginStats (or other approach) go through alignments and spit out the...

Braker3/GeneMark-ETP: file not found: complete.gtf, complete.id, complete_uniq.gtf

52

Hello, Thank you for all the great tools coming from this team. I gave Braker3 a shot, but am running into an error at the moment. I will report below...

STAR vs HiSat2 for RNA-seq data in Braker3

3

Hi again, For Braker1, I had been providing BAM files produced by STAR. Since you are now using StringTie assembly as part of the Braker pipeline, I was wondering if...

Not out of the woods yet: uninitialized values, can't open TGA.mat, and more.

4

Hi again, I am starting a new issue here as it is technically now a new issue, but this is still part of my journey established in now-monstrous-in-size recent threads:...

Hello, Thanks for the wonderful, absolutely fantastic program. I've used it for a regular liftover job from one genome version to another for a non-model organism.. and it was just......

Question: window-length pros and cons

3

Hi, RaCon is great. I was wondering if there were pros and cons to the ```--window-length``` parameter, which is 500bp by default. I tested 5kb -- so I know it...

Meaningful MAPQ values would be excellent.

4

Hi all, I am trying out Magic-BLAST for mapping short-reads, and may want to test it in various pipelines. I noticed, however, that the MAPQ field in the SAM output...

Hi, Apologies in advance: I have a tangential question about quiver polishing my Falcon assembly. I know this is not necessarily the place for such a question, but I have...