Description

Compare, merge, annotate and estimate accuracy of generated gtf files

Input

Name (Type)
Description
Pattern

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}

fasta (file)

Genome reference fasta file (optional)

*.{fasta,fa}

fai (file)

Index for fasta file

*.fai

reference_gtf (file)

Reference annotation in gtf/gff format (optional)

*.{gtf,gff}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing meta data
e.g. [ id:‘test’, single_end

]

annotated_gtf (file)

Annotated gtf file when reference gtf is provided (optional)

*.annotated.gtf

combined_gtf (file)

Combined gtf file when multiple input files are
provided (optional)

*.annotated.gtf

tmap (file)

File listing the most closely matching reference transcript
for each query transcript (optional)

*.tmap

refmap (file)

File listing the reference transcripts with overlapping
query transcripts (optional)

*.refmap

loci (file)

File with loci

*.loci

stats (file)

File with stats for input transcripts as compared to
reference alternatively stats for the combined gtf

*.stats

tracking (file)

This file matches transcripts up between samples

*.tracking

versions (file)

File containing software versions

versions.yml
author
Github user jemten
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