Re-defining Cgigas Canonical features

Below is an updated version of canonical genome tracks as part of the qdod project – @ github. Updates include details on version 25 gff files and adding the TE track derived via WU-Blast.

Canonical Feature Tracks (Ensembl)

Ensemble provides a feature tracks that are updated on a regular basis.
They can be directly accessed at
ftp://ftp.ensemblgenomes.org/pub/current/metazoa/gff3/crassostrea_gigas/
ftp://ftp.ensemblgenomes.org/pub/current/metazoa/gtf/crassostrea_gigas/
Note this will ensure you have the most current version.

Version 25
GTF

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.gtf

GFF3

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.25.gff3

Screenshot

List of gff feature (v25)

5 EnsemblGenomes RNA
2530 EnsemblGenomes exon
13 EnsemblGenomes gene
28 EnsemblGenomes miRNA
28 EnsemblGenomes miRNA_gene
1410 EnsemblGenomes pseudogenic_tRNA
13 EnsemblGenomes rRNA
13 EnsemblGenomes rRNA_gene
47 EnsemblGenomes snRNA
47 EnsemblGenomes snRNA_gene
20 EnsemblGenomes snoRNA
20 EnsemblGenomes snoRNA_gene
994 EnsemblGenomes tRNA_gene
2422 EnsemblGenomes transcript
186890 GigaDB CDS
186938 GigaDB exon
26101 GigaDB gene
26101 GigaDB transcript
650376 dust repeat_region
224899 trf repeat_region

Canonical Feature Tracks (version 9)

Gene

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff

Exons

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff

Intron

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff

Promoter (= 1kbp 5′ of genes)

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff

Transposable Elements

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff

Complement to Gene, Promoter, and TE tracks

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed

All CGs

http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff

Screenshot:

Details regarding the development of these tracks can be found in this IPython Notebook as well as in this methods section.

quicklook

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff <==
C16582  flankbed    promoter    386 395 .   -   .   ID=CGI_10000001;
C17212  flankbed    promoter    1   30  .   +   .   ID=CGI_10000002;
C17316  flankbed    promoter    1   29  .   +   .   ID=CGI_10000003;

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff <==
scaffold38980   fuzznuc nucleotide_motif    63420   63421   2   +   .   ID=scaffold38980.741;note=*pat pattern:CG
scaffold38980   fuzznuc nucleotide_motif    63670   63671   2   +   .   ID=scaffold38980.742;note=*pat pattern:CG

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE-WUBLASTX.gff <==
scaffold1479    WUBlastX    LTR_Gypsy   2608    4209    104 +   .   .
C33730  WUBlastX    LTR_Pao 1960    2589    652 -   .   .
C33730  WUBlastX    LTR_Pao 3358    5868    1471    -   .   .

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff <==
C21242  TRF Tandem_Repeat   38  100 72  +   .   .
C21306  TRF Tandem_Repeat   35  143 112 +   .   .
C21306  TRF Tandem_Repeat   574 947 208 +   .   .

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TEx.gff <==
scaffold1479    WUBlastX    LTR_Gypsy   2608    4209    104 +   .   .
C33730  WUBlastX    LTR_Pao 1960    2589    652 -   .   .
C33730  WUBlastX    LTR_Pao 3358    5868    1471    -   .   .

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff <==
C16582  GLEAN   CDS 35  385 .   -   0   Parent=CGI_10000001;
C17212  GLEAN   CDS 31  363 .   +   0   Parent=CGI_10000002;
C17316  GLEAN   CDS 30  257 .   +   0   Parent=CGI_10000003;

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff <==
C16582  GLEAN   mRNA    35  385 0.555898    -   .   ID=CGI_10000001;
C17212  GLEAN   mRNA    31  363 0.999572    +   .   ID=CGI_10000002;
C17316  GLEAN   mRNA    30  257 0.555898    +   .   ID=CGI_10000003;

==> /Volumes/web/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff <==
C17476  subtractBed intrn   75  103 .   -   .   Parent=CGI_10000004;
C19392  subtractBed intrn   184 451 .   +   .   Parent=CGI_10000015;
C20262  subtractBed intrn   539 641 .   -   .   Parent=CGI_10000025;