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 reference (fasta) and annotated genome (gtf) from https://www.pseudomonas.com/strain/download
2b. I unpacked the files since they are in .x.gz format
- I used the tool hisat2 for the alignment of reads to the mentioned genome reference (fasta)
- I tried to link the aligned counts (hisat2 files) to genes with the annotated genome (gtf) and the tool featureCounts
The job was cancelled and I got following error code: "Fatal error: Exit code 255 (). ERROR: no features were loaded in format GTF. The annotation format can be specified by the ‘-F’ option, and the required feature type can be specified by the ‘-t’ option…
The porgram has to terminate. "
The error code mentions something with format GTF. I double checked and the annotated reference genome was in the correct format. Maybe I did something along the line that I was not supposed to do.
Im relatively new to galaxy and I would very much appreciate your help.