Hello Galaxy Community, Im doing a RNASeq Analysis and having problems with the tool featureCounts. I will give a short overview of what Ive done so far and what error I get at the end. I checked the quality of my rnaseq files with FASTQC tool Since I Work with Pseudomonas I downloaded the genome…

Hi @Marcel and @q_thistle , the problem is that by default featureCounts set exon as feature filter (Advanced options/GFF feature type filter), but this feature doesn’t appear in the Pseudomonas annotation file (third column). You need to specify CDS as feature type in featureCounts. Regards

Problems with the tool featureCounts: Fatal error: Exit code 255 ()

usegalaxy.org support

jennaj November 17, 2022, 12:25am 5

Hi @Mila

If adjusting the tool setting is not enough, the problem could be with one or more of the input formats. These three FAQs tend to help.

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Fatal INPUT FILE error, no valid exon lines in the GTF file usegalaxy.org support	0	1165	March 25, 2021
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Problems with the tool featureCounts: Fatal error: Exit code 255 ()

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