FeatureCounts Persistent Fatal error: Exit code 255

[igor]

Hi Adriana,
check this thread:

hisat2 and featurecounts

Hi all, [Screen Shot 2022-05-05 at 2.42.17 PM] [Screen Shot 2022-05-05 at 2.42.38 PM] I am trying to align my RNA-seq reads (Bacteria), using HISAT2 to a reference genome (assembly.fna). Then,to measure the expression in the resulted bam.file, I used (featurecounts) tool, using the (gtf) annotation file. However, although both fna/gtf files belong to the same strain tested, I got this empty report; Your help much appreciated

Is it similar to your situation?
If you work with hg38, consider using featureCounts with built-in gene model

Transcriptomics / Hands-on: 1: RNA-Seq reads to counts

You can also post a fragment of the gene annotation you use with featureCounts.

I get reliable results with GenCode annotations.

Hope that helps.

Kind regards,
Igor