Christoffer Flensburg

Ok, I made superFreq check the version of Rsubread and use the appropriate syntax.... Hopefully should work for all versions now. Update superFreq and try again, let me know how...

Hey! Looks good! Genomes are pushing the limits for superFreq, so you have to be quite careful with resource settings. We run a 30x cancer-normal human genome start to end...

Hey. THe error message isn't very informative, I need the logfile in R/[individual]/runtimeTracking.log. Note that this file includes your metadata, but no identifying variants.

Hi! Thanks for sending through, and sorry for delay. Busy days this week... I don't see any red flags in the log files, except that you're not running on the...

Tests failed because of a typo on my end, `%in$` instead of `%in%`. 🙄 You'll have to wait one more day it seems. Oof.

Ok, tests passed well enough. One sample failed, but that's because I had deleted the reference normals, so I'll forgive superFreq for that. I got an informative error message at...

Ok, yep, the version error is expected. I added the 4.0.0 requirement as I've only been testing and supporting on that for a while, so high time to make it...

As this is a conflict with featureCounts, I need to know which version of featureCounts (Rsubread package, look in sessionInfo()) you are running so that I can try to reproduce...

Thanks. That version worked in our tests, so not sure where the error is. I checked the featureCounts documentaiton and doesn't seem anything has changed in the way superFreq is...

Hi! Sorry for the delay. Hmm, seems it's a Rsubread version conflict with your BAM file. :/ The last featureCounts call doesn't have anything to do with superFreq, so very...