Featurecounts error with reference GTF file

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1

Hi, I’m troubleshooting an RNA-seq analysis in Galaxy and am running into an error at the featureCounts step.

I am analyzing Xenopus laevis RNA-seq data and uploaded both the reference genome FASTA file and the corresponding GTF annotation file downloaded from Xenbase . Since both files came from the same Xenbase reference set, I believe the genome and annotation should match.

When I run featureCounts using the uploaded GTF file, I receive the following error:

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HI @Xxl

This topic was addressed on this forum many times. Check the error message at the end of the log file. It seems the annotation file has different attribute for genes (not gene_id). You probably can resolve the issue by using attribute present in the annotation file. Search the forum for more info.

Kind regards,

Igor