I currently have two issues when running with gffcompare v0.12.2:
I understand that the tmap and refmap files should be in the query gff directory, but upon running the code, I find that there are no files in the directory or any other relevant directories. Could you please help me understand what is going wrong?
Total union super-loci across all input datasets: 14959
(12405 multi-transcript, ~8.4 transcripts per locus)
125784 out of 125784 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant)
I do get the loci, stats, tracking and combined.gtf files.
Any help on these two issues would be greatly appreciated!
Thank you
Hi there,
Thank you for creating this wonderful tool!
I currently have two issues when running with gffcompare v0.12.2:
I ran this code:
gffcompare -r /data/gpfs/projects/punim1466/db/refdata-gex-GRCh38-2020-A/genes/genes.gtf -i "/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff.txt"
And in 'gff.txt' I have the following:
gffcompare v0.12.2 | Command line was:
gffcompare -r /data/gpfs/projects/punim1466/db/refdata-gex-GRCh38-2020-A/genes/genes.gtf -i /data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff.txt
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Total union super-loci across all input datasets: 14959 (12405 multi-transcript, ~8.4 transcripts per locus) 125784 out of 125784 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant)