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.)
Inputs
Name | Type & Properties | Description |
|---|---|---|
--genscan -g | file required | Input genscan bed file that will be converted. |
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. |
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). |
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 v0.3.1 \
-main-script target/nextflow/agat/agat_convert_genscan2gff/main.nf \
-params-file params.yaml Relationships
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Current component
agat/agat_convert_genscan2gffbiobox v0.3.1
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