Tool update: featureCounts

[teresa-m]

Hi All,

today while running the following GTN tutorial, we discovered a not user-friendly behavior of how FeatureCounts allows users to use the build in references.

The tutorial asks to:

• add the input Alignment file -> a BAM collection
• then Gene annotation file should be set to -> featureCounts built-in option
• and mm10 should be selected. However, this was not possible:

But:

• if one sets the Gene annotation file to -> featureCounts built-in first,
• and then select the input It was possible to select the reference genome.

Could someone have a look here? Thanks a lot!

[bernt-matthias]

Have you set the dbkey of your BAM files (to mm10)? https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_change_dbkey.html

Would be interesting to know if setting or changes anything.

[teresa-m]

The mm10 is already specified as db: https://usegalaxy.eu/u/teresa-m/h/copy-of-rna-seq-reads-to-counts I did not run the training my self. This is a copy from the history of one of the GTA participants who followed this training.

[bernt-matthias]

Seems to work nicely with single datasets:

Screencast from 25.10.2024 10:30:13.webm

Problem seems to occur only for collections:

Screencast from 25.10.2024 10:33:23.webm

Guess this needs a fix in Galaxy itself.