I generated the reference and gtf file with 10x as suggested. I then renamed the headers in the reference file to keep only the IDs with no description. I'm not sure why it says 'improper genomic coordinate 1026 on NC_001913.1 for NC_001913.1.stringtie.1.1' and how could I fix this?
I'm running the epi2me oxford nanopore single cell analysis pipeline and get this stringtie error:
Caused by: Process pipeline:process_bams:stringtie (1) terminated with an error exit status (1)
Command executed: Add chromosome label (-l) to generated transcripts so we don't get name collisions during file merge later samtools view -h align.bam NC_001913.1 | tee >( stringtie -L -c 2 -p 8 -G chr.gtf -l "NC_001913.1.stringtie" -o "stringtie.gff" - ) | samtools fastq | bgzip --threads 2 -c > reads.fastq.gz Get transcriptome sequence gffread -g ref_genome.fa -w "transcriptome.fa" "stringtie.gff"
Command exit status: 1 Command output: (empty) Command error: [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 333717 reads GffObj::getSpliced() error: improper genomic coordinate 1026 on NC_001913.1 for NC_001913.1.stringtie.1.1
I generated the reference and gtf file with 10x as suggested. I then renamed the headers in the reference file to keep only the IDs with no description. I'm not sure why it says 'improper genomic coordinate 1026 on NC_001913.1 for NC_001913.1.stringtie.1.1' and how could I fix this?