agat/agat_sp_statistics
gene annotations
statistics
gff
Description
The script provides exhaustive statistics of a gft/gff file.
If you have isoforms in your file, even if correct, some values calculated
might sounds incoherent: e.g. total length mRNA can be superior than the
genome size. Because all isoforms length is added... It is why by
default we always compute the statistics twice when there are isoforms,
once with the isoforms, once without (In that case we keep the longest
isoform per locus).
Inputs
Name | Type & Properties | Description |
|---|---|---|
--gff -i | file required | Input GTF/GFF file. |
--gs_fasta | file | Genome size directly from a fasta file to compute more statistics. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | The file where the results will be written. |
Options
Name | Type & Properties | Description |
|---|---|---|
--plot -p -d | boolean_true | When this option is used, an histogram of distribution of the features will be printed in pdf files. |
--gs_size | integer | Genome size in nucleotides to compute more statistics. |
--verbose -v | integer | Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3 are increasing 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.txt"
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_sp_statistics/main.nf \
-params-file params.yaml Relationships
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Current component
agat/agat_sp_statisticsbiobox v0.4.2
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