Please advise how to proceed. I mapped the read of RNAseq to the genome with hisat2, and then cufflinks with Galaxy, but cuffmerge in Galaxy of GTF file is an error and I am in trouble.
Contents GTF file (s) produced by Cufflinks 28: assembled transcripts, 39: assembled transcripts, 45: assembled transcripts Use Reference Annotation Yes Reference Annotation 25: Xenobase_gene_model.gff3.txt Use Sequence Data No Minimum isoform fraction 0.05 Job Resource Parameters
The error message is Error running cuffmerge:
[Wed Aug 14 19:27:50 2019] Beginning transcriptome assembly merge
[Wed Aug 14 19:27:50 2019] Preparing output location cm_output / [Wed Aug 14 19:28:06 2019] Converting GTF files to SA