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