search

gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
MIT License
198 stars 32 forks source link

Missing tmap and refmap files in query gff directory + missing statistics in stats file #72

Open jchang97 opened 2 years ago

jchang97 commented 2 years ago

Hi there,

Thank you for creating this wonderful tool!

I currently have two issues when running with gffcompare v0.12.2:

  1. 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?

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:

/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libA/isoform_annotated.filtered_libA.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libB/isoform_annotated.filtered_libB.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libC/isoform_annotated.filtered_libC.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libD/isoform_annotated.filtered_libD.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libE/isoform_annotated.filtered_libE.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libF/isoform_annotated.filtered_libF.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libG/isoform_annotated.filtered_libG.gff3
/data/gpfs/projects/punim1466/analysis/nanopore/isoform/novel_isoforms/gff/libH/isoform_annotated.filtered_libH.gff3
  1. The output in my stats file are missing the percentages and only show:

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

#

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