Description

Generate tables of feature metadata from GTF files

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing information on input GTF file
e.g. [ id:‘test’ ]

meta2 (map)

Groovy Map containing information in input FASTA file
e.g. [ id:‘test’ ]

gtf (file)

gtf annotation file

*.{gtf}

fasta (file)

An optional cDNA file for extracting meta info and/or filtering.

*.{gtf}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

feature_annotation (file)

TSV file with feature annotation

*.{tsv}

filtered_cdna (file)

Where —parse-cdnas is specified in ext.args and an input fasta file is
provided, filtered sequences are output to the specified file. No file
will be output if this is not specified (for example for use of
—dummy-from-cdnas only). See documentation at
https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation.

*.{tsv}
included in
differentialabundance
author
Github user pinin4fjords
get in touch
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Tools

atlasgeneannotationmanipulation
Apache-2.0

Scripts for manipulating gene annotation

github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation