Hi @matt_m
Thanks for sharing your history!
How to review work is explained in a few topics, including this one.
For your shared history, let’s look at featurecounts dataset 72.
Clicking into the job details pages (i-info icon) to review the error message shows this content.
This part of the message is reporting about the content of the inputs.
ERROR: Paired-end reads were detected in single-end read library
Then scrolling up a bit on that same view to review the original parameters, it looks like you need to toggle a parameter when you rerun. Paired end will better describe the content to be counted up per feature.
Then, to do things like confirming the reference data, this is a good guide to follow.
Inspecting your sequence identifiers, it looks like your BAM and GTF are from the same genome assembly. The parameters on the Featurecounts form are set up for a GTF file.
The only thing I notice is that you might need to remove the extra # header lines from the GTF. This is what was causing the problem with the gffread run dataset 74. You can run your files through that tool but you might not need it.
Tutorial examples can be found here.
More about preparing reference data can be found under these tags.
Hope this helps! 