Compare, merge, annotate and estimate accuracy of generated gtf files
meta{:bash}
:map
Groovy Map containing meta data e.g. [ id:‘test’, single_end:false ]
gtfs{:bash}
:file
GTF/GFF files e.g. [ ‘file_1.gtf’, ‘file_2.gtf’ ]
*.{gtf,gff}
meta2{:bash}
fasta{:bash}
Genome reference fasta file (optional)
*.{fasta,fa}
fai{:bash}
Index for fasta file
*.fai
meta3{:bash}
reference_gtf{:bash}
Reference annotation in gtf/gff format (optional)
annotated_gtf{:bash}
*.annotated.gtf{:bash}
Annotated gtf file when reference gtf is provided (optional)
*.annotated.gtf
combined_gtf{:bash}
*.combined.gtf{:bash}
Combined gtf file when multiple input files are provided (optional)
tmap{:bash}
*.tmap{:bash}
File listing the most closely matching reference transcript for each query transcript (optional)
*.tmap
refmap{:bash}
*.refmap{:bash}
File listing the reference transcripts with overlapping query transcripts (optional)
*.refmap
loci{:bash}
*.loci{:bash}
File with loci
*.loci
stats{:bash}
*.stats{:bash}
File with stats for input transcripts as compared to reference alternatively stats for the combined gtf
*.stats
tracking{:bash}
*.tracking{:bash}
This file matches transcripts up between samples
*.tracking
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
GffCompare by Geo Pertea
