featurecounts error using BAM and gff3 files

[jennaj]

Hi @Luisa_Nieto

Let’s please continue in your original topic. Please try the advice given first. It solves most if not all technical errors. Scientific content problems are different but you can’t troubleshoot those until the technical are resolved.

Be aware that GFF3 doesn’t always work well – GTF always does when the formatting is right. If you want to share a link to your history, that would help. Post that back into a reply in that topic please. If you’d rather not post that publicly, ask for a moderator to start up a private message chat to use instead.

new annotated bacterial genome

Hi @Luisa_Nieto Thanks for explaining Use a custom genome fasta and optionally promote that to a custom build to create a “database” metadata that be assigned to datasets. Some tools use the fasta directly and some tools require/use the “database” metadata. Tip: avoid assigning an existing “database” to any data that is associated with a custom genome fasta – instead create your own custom database key to avoid content conflicts that can be difficult to interpret. The general f…