/volume2/web/Atumefaciens/20220419-pgen-gene_annotation_mapping

Directory for creating a canonical gene annotation file for our P.generosa genome.

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20220419-pgen-accession-gene_name-gene_description-go_ids.tab: Tab-delimited file containing data parsed from 20220419-pgen-uniprot_batch-results.txt. Column contents:

- SPIDs
- gene name
- gene description
- gene ontology IDs

20220419-pgen-gene-accessions-gene_id-gene_name-gene_description-alt_gene_description-go_ids.tab: Tab-delimited file containing join of 20220419-pgen-accession-gene_name-gene_description-go_ids.tab and 
Panopea-generosa-v1.0.a4-blast-diamond-functional-genome_IDs-SPIDs.txt. Column contents:

- `gene_ID`: Gene ID from our Panopea generosa genome.

- `SPIDs`: Comma-delimited list of SPIDs from UniProt. One SPID in this list is a match corresponding to the our original BLAST annotations.

- `UniProt_gene_ID`: Gene accession from UniProt.

- `gene`: Abbreviated gene name from UniProt.

- `gene_description`: Human-readable gene description from UniProt.

- `alternate_gene_description`: Human-readable alternate gene description from UniProt.

- `GO_IDs`: GO IDs from UniProt.


20220419-pgen-uniprot_batch-results.txt: UniProt accession files for all SPIDs in Panopea-generosa-v1.0.a4-blast-diamond-functional-SPIDs.txt. UniProt automatically eliminates duplicate SPIDs and only returns
unique entries.

Panopea-generosa-v1.0.a4-blast-diamond-functional-SPIDs.txt: List of SwissProt IDs identified in Panopea-generosa-v1.0.a4-blast-diamond-functional_best.tab.

Panopea-generosa-v1.0.a4-blast-diamond-functional-genome_IDs-SPIDs.txt: Tab-delimited list of P.generosa genome genes and corresponding SPIDs from Panopea-generosa-v1.0.a4-blast-diamond-functional_best.tab.

Panopea-generosa-v1.0.a4-blast-diamond-functional.tab: Concatenation of BLAST and DIAMOND BLAST annotations generated during our GenSAS genome annotation. Format is standard BLAST output format 6.

Panopea-generosa-v1.0.a4-blast-diamond-functional_best.tab: Best BLAST/DIAMOND BLAST matches for each P.generosa gene, based on e-value, from Panopea-generosa-v1.0.a4-blast-diamond-functional.tab. 


Notebook:

https://robertslab.github.io/sams-notebook/2022/04/19/Data-Wrangling-Create-Primary-P.generosa-Genome-Annotation-File.html