agat/agat_convert_genscan2gff

gene annotations

GFF conversion

GENSCAN

Description

The script takes a GENSCAN file as input, and will translate it in gff
format. The GENSCAN format is described here.

Known problem

You must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA
sequences and does not crash/warn if an header is submited along the
sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
nucleotides of the sequence. Then all prediction location are shifted
accordingly. (checked only on the online version.
I don't know if there is the same problem elsewhere.)

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

GFF conversion

GENSCAN

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.gff"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/agat/agat_convert_genscan2gff/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--genscan -g	file required	Input genscan bed file that will be converted.

Name

Type & Properties

--genscan

-g

file

required

Outputs

Name	Type & Properties	Description
--output -o --out --outfile --gff	file required output	Output GFF file. If no output file is specified, the output will be written to STDOUT.

Name

Type & Properties

--output

-o

--out

--outfile

--gff

file

required

output

Arguments

Name	Type & Properties	Description
--source	string	The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
--primary_tag	string	The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
--inflate_type	string	Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
--verbose	boolean_true	add verbosity
--config -c	file	AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

Name

Type & Properties

--source

string

--primary_tag

string

--inflate_type

string

--verbose

boolean_true

--config

-c

file