Alexander Bender

A reason can be that QC was not done properly and you try to run the function on cells without any counts, meaning all gene in that cell are zero....

Just wanted to add this as the above script worked decently in the past but fails with more recent versions such as Bioconductor 3.14 and Rocker 4.1.2 images, error like:...

When running e.g. Bioc 3.14 on a HPC via Singularity with the command as in my previous comment I now at times get lots of log messages like below. R...

I managed to build mosdepth on Mac (10.14.6), see https://www.biostars.org/p/437365/ plus Brent now provides some non-static binaries, https://github.com/brentp/mosdepth/issues/103#issuecomment-627028723

Thanks @rob-p for opening the issue. Just as a comment, I was wrong to assume that the additional barcode was in R1, and it's called Probe BC, not pCS1, sorry...

+1 though a duplicate of https://github.com/COMBINE-lab/alevin-fry/issues/85 Flex is the rebranded name of what formerly was 'Fixed RNAAssay Kit'.

This is probably multithreading by BLAS (https://stackoverflow.com/questions/17053671/how-do-you-stop-numpy-from-multithreading) at least this is what I often see (and have to explicitely disable) in R on machines that have a multithread-ready BLAS library...

Make sure your input count matrix is a matrix, not a data.frame. Related: https://support.bioconductor.org/p/9154478/#9154480

Is there any progress on this issue, calling replicate samples without input controls?

@kiwipeel Simple run `identifyOverExpressedGenes()` and then inspect how `[email protected]` is formatted. You can then modify that slot and populate with your custom DE results, matching that format.