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suryasaha/Funcional_annotation_README

Last active February 19, 2021 16:28
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README template for funtional annotation files
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Funcional_annotation_README
The files in this directory represent functional annotations of the following dataset:
https://i5k.nal.usda.gov/data/Arthropoda/phopyr-%28Photinus_pyralis%29/Ppyr1.3/2.Official%20or%20Primary%20Gene%20Set/Photinus_pyralis_Annotation_Release_100/GCF_008802855.1_Ppyr1.3_cds_from_genomic.fna.gz
Information about the functional annotation process can be found here: https://agbase-docs.readthedocs.io/en/latest/
The file GCF_008802855.1_Ppyr1.3_cds_from_genomic.fna.gz was processed with agbase/goanna:2.2 (https://hub.docker.com/repository/docker/agbase/goanna/tags?page=1) docker container to generate GO functional annotation. GOanna was run with the following parameters: -a invertebrates -b yes -g 70 -x 7054 -k 9 -q 70 -r 1.2. Please see the documentation for details at https://agbase-docs.readthedocs.io/en/latest/goanna/intro.html#help-and-usage-statement
The resulting files are:
GCF_008802855_GOanna.asn
GCF_008802855_GOanna.html
GCF_008802855_GOanna_gaf.tsv
GCF_008802855_GOanna_out.tsv
The file GCF_008802855.1_Ppyr1.3_cds_from_genomic.fna.gz was processed with agbase/interproscan:5.45-80.0_0 (https://hub.docker.com/repository/docker/agbase/interproscan/tags?page=1) docker container to generate GO and pathway functional annotation. InterProSCan was run with the following parameters: -g -l -p -n -x 7054. Please see the documentation for details at https://agbase-docs.readthedocs.io/en/latest/interproscan/intro.html#help-and-usage-statement
The resulting files are:
GCF_008802855_interproscan_acc_go_counts.txt
GCF_008802855_interproscan_acc_interpro_counts.txt
GCF_008802855_interproscan_acc_pathway_counts.txt
GCF_008802855_interproscan_GOanna_combined.gaf.tsv
GCF_008802855_interproscan_go_counts.txt
GCF_008802855_interproscan_interpro_counts.txt
GCF_008802855_interproscan_pathway_counts.txt
The file GCF_008802855.1_Ppyr1.3_cds_from_genomic.fna.gz was processed with agbase/kobas:3.0.3_0 (https://hub.docker.com/repository/docker/agbase/kobas/tags?page=1) docker container with the annotate option to generate pathway functional annotation.
The resulting files are:
GCF_008802855_kobas-annotate
GCF_008802855_kobas-annotate_acc_pathways.tsv
GCF_008802855_kobas-annotate_pathways_acc.tsv
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