Comments (2)
Here's the head of the .gff:
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ASM557713v1
#!genome-build-accession NCBI_Assembly:GCF_005577135.1
#!annotation-date 10/08/2023 12:45:54
#!annotation-source NCBI RefSeq
##sequence-region NZ_CP040360.1 1 3081514
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2579791
NZ_CP040360.1 RefSeq region 1 3081514 . + . ID=NZ_CP040360.1:1..3081514;Dbxref=taxon:2579791;Is_circular=true;Name=ANONYMOUS;collection-date=2017-04-17;country=Singapore: near Pulau Ubin;culture-collection=PCC:11901;gbkey=Src;genome=chromosome;isolation-source=estuarine water [ENVO:01000301];lat-lon=1.421583 N 103.955722 E;mol_type=genomic DNA;old-name=Synechococcus sp. NTU 1704;strain=PCC 11901
NZ_CP040360.1 RefSeq gene 1 378 . + . ID=gene-FEK30_RS01170;Name=FEK30_RS01170;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01170;old_locus_tag=FEK30_01170
NZ_CP040360.1 GeneMarkS-2+ CDS 1 378 . + 0 ID=cds-WP_138071278.1;Parent=gene-FEK30_RS01170;Dbxref=GenBank:WP_138071278.1;Name=WP_138071278.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FEK30_RS01170;product=hypothetical protein;protein_id=WP_138071278.1;transl_table=11
NZ_CP040360.1 RefSeq gene 375 1010 . - . ID=gene-FEK30_RS01175;Name=FEK30_RS01175;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01175;old_locus_tag=FEK30_01175
NZ_CP040360.1 GeneMarkS-2+ CDS 375 1010 . - 0 ID=cds-WP_138071280.1;Parent=gene-FEK30_RS01175;Dbxref=GenBank:WP_138071280.1;Name=WP_138071280.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FEK30_RS01175;product=hypothetical protein;protein_id=WP_138071280.1;transl_table=11
NZ_CP040360.1 RefSeq gene 1086 2045 . - . ID=gene-FEK30_RS01180;Name=FEK30_RS01180;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01180;old_locus_tag=FEK30_01180
NZ_CP040360.1 Protein Homology CDS 1086 2045 . - 0 ID=cds-WP_138071282.1;Parent=gene-FEK30_RS01180;Dbxref=GenBank:WP_138071282.1;Name=WP_138071282.1;Ontology_term=GO:0016491,GO:0016651;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA,oxidoreductase activity%2C acting on NAD(P)H|0016651||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_013320252.1;locus_tag=FEK30_RS01180;product=Gfo/Idh/MocA family oxidoreductase;protein_id=WP_138071282.1;transl_table=11
NZ_CP040360.1 RefSeq gene 2162 2455 . + . ID=gene-FEK30_RS01185;Name=FEK30_RS01185;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01185;old_locus_tag=FEK30_01185
NZ_CP040360.1 Protein Homology CDS 2162 2455 . + 0 ID=cds-WP_138071284.1;Parent=gene-FEK30_RS01185;Dbxref=GenBank:WP_138071284.1;Name=WP_138071284.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017320150.1;locus_tag=FEK30_RS01185;product=ferredoxin;protein_id=WP_138071284.1;transl_table=11
NZ_CP040360.1 RefSeq gene 2819 3112 . + . ID=gene-FEK30_RS01190;Name=petF1;gbkey=Gene;gene=petF1;gene_biotype=protein_coding;locus_tag=FEK30_RS01190;old_locus_tag=FEK30_01190
NZ_CP040360.1 Protein Homology CDS 2819 3112 . + 0 ID=cds-WP_012307922.1;Parent=gene-FEK30_RS01190;Dbxref=GenBank:WP_012307922.1;Name=WP_012307922.1;gbkey=CDS;gene=petF1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017320150.1;locus_tag=FEK30_RS01190;product=ferredoxin PetF1;protein_id=WP_012307922.1;transl_table=11
from snakemake-crispr-guides.
I'm not aware of many more different types of annotation.
But you're right, in principle it should be possible to get features from various different sources. The default options are really just what I have encountered personally.
Can you paste the head of your annotation here? Would be useful to understand how this looks like.
I can imagine to simply add a list of different valid options/tags in the config.yml
file. Then users can add their own when needed.
from snakemake-crispr-guides.
Related Issues (19)
- Add functionality to deal with guides targeting multiple loci (e.g. duplicated) genes
- Feature requests: add function to design random control guide RNAs HOT 1
- improve flexibility of handling `gff` input files
- add feature to export guide list as GFF file for visualization
- When using assembly: "GCF_005577135.1", species name is not parsed correctly, which is causing failure in create_bsgenome.R and design_guides.R HOT 4
- Feature request: add CRISPRoff score HOT 1
- add possibility to create guides by tiling only, or by tiling for intergenic regions (mixed) HOT 1
- workflow is listed in snakemake wf catalog, but not as "standardized usage" HOT 3
- feature request: option to add additional space around CDS when designing intergenic guides
- improve output figures for intergenic regions when using tiling approach
- Feature request: add score based on distance to TSS
- change license to MIT
- Add module to generate BSgenome --> enables bowtie as default off-target search HOT 1
- Feature request: add score based on G content of seed region
- Testing fails on GH actions with snakemake test workflow
- Test behavior with alternative options HOT 1
- add overview figures for pipeline and guide RNA localization on strands
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from snakemake-crispr-guides.