I used featureCounts about two weeks ago on one dataset and had no issues. Today I tried running featureCounts on a different set of data and the annotation file that we used from UCSC does not show up as an option anymore. It is still in my history from when I used it two weeks ago so I am very confused as to why it does not work anymore. Has this happened to anyone else recently?
The Featurecounts tool now requires that the database metadata assignment is made to both the BAM and GTF inputs.
Please see this post for full details: https://biostar.usegalaxy.org/p/24154/#28027
Thanks! Jen, Galaxy team
The tool was recently upgraded to version 126.96.36.199 and the tool form changed slightly. I tested this same option last night/early this morning and it worked at Galaxy Main https://usegalaxy.org. Details: https://github.com/galaxyproject/usegalaxy-playbook/issues/52
To use your own annotation, try setting the option "Gene annotation file" to be "in your history". Appropriate inputs will be listed in the select menu. If you do not see it, double check that the UCSC reference annotation has the datatype
Thanks and let us know if that does not solve the problem! Jen, Galaxy team