Hello. I’m running FeatureCounts with BAM files I sorted using SamTools Sort (along with creating index .bai for each BAM file). I’m using a uploaded genome.gtf file which matches the genome I used for mapping with Bowtie2. But when I run feature counts, I get the error “an error occurred with this dataset: format tabular” and I need help figuring it out.
I used ChatGPT to try and figure it out and it seems like my BAM files are correct, the gtf file is formatted correctly, and over 98% of the genes were mapped. Otherwise I haven’t been able to troubleshoot it and could use some help. Ideally I would like to not post my history publicly, if it’s possible to do so privately but whatever gets this issue sorted.
Hi @matt_m,
If you created BAM files in Galaxy, sorting is not required: by default, BAM files in Galaxy are coordinate-sorted. Check the command box in Info section: you’ll see smatools sort in the command/pipeline.
As for the error: it is hard to say what is going on. Can you share the history here? If you have many file, just copy one sample into a new history. To share the history, click at History options (three horizontal bars icon) in the top right corner of the history panel > Share or Publish > In the middle window Make this history accessible and paste the URL into reply. Make sure that the annotation file is present in the shared history.