###Canonical Feature Tracks (Ensembl) Ensemble provides a feature tracks that are updated on a regular basis. They can be directly accessed at 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 ![igv_en](http://eagle.fish.washington.edu/cnidarian/skitch/IGV_1942079F.png) 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: ![shot](http://eagle.fish.washington.edu/cnidarian/skitch/IGV_and_trilobite_1AA0CD8A.png) _Details regarding the development of these tracks can be found in [this IPython Notebook](http://nbviewer.ipython.org/github/sr320/ipython_nb/blob/master/TJGR_OysterGenome_IGV.ipynb) as well as in this [methods section](https://peerj.com/articles/215/#p-7)._ 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; ``` *** ##Experimental Feature Tracks ###_Crassostrea gigas_ high-throughput bisulfite sequencing (gill tissue) Citation: Gavery, Mackenzie; Roberts, Steven (2013): Crassostrea gigas high-throughput bisulfite sequencing (gill tissue). figshare. This fileset contains genomic feature tracks from **methylation-enriched** high-throughput bisulfite sequencing and RNA-seq analysis for Pacific oyster (Crassostrea gigas) gill tissue. Feature tracks were developed to be viewed with Integrative Genomics Viewer (http://www.broadinstitute.org/igv/) in conjunction with the C. gigas genome (Fang et al. 2012). All data and instructions are also available at . Associated Publicaiton: XXXXXXX File descriptions: [BiGill_CpG_methylation.igv](http://files.figshare.com/1252773/BiGill_CpG_methylation.igv) - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [BiGill_exon_clc_rpkm.igv](http://files.figshare.com/1252772/BiGill_exon_clc_rpkm.igv) - Exon-specific gene expression values (RPKM) from RNA-seq analysis. [BiGill_igv_charlie.xml](http://files.figshare.com/1252770/BiGill_igv_charlie.xml) - A session file, which loads methylation and RNA-seq feature tracks as well as the location of C.gigas genome features. [Query to derive_CG_AllData_IGV.txt](http://files.figshare.com/1252771/Query_to_derive_CG_AllData_IGV.txt) - Query (SQLShare) used to derive the methylation feature track from the original methratio output (http://goo.gl/5LGq9Q) Screenshot ![shot](http://eagle.fish.washington.edu/cnidarian/skitch/IGV_-_Session__http__eagle.fish.washington.edu_trilobite_Crassostrea_gigas_v9_tracks_BiGill_igv_charlie.xml_180F2D2E.png) *** ###_Crassostrea gigas_ high-throughput bisulfite sequencing (male gamete) This file contains genomic feature tracks from high-throughput bisulfite sequencing for Pacific oyster (Crassostrea gigas) male gonad tissue. Feature tracks were developed to be viewed with Integrative Genomics Viewer (http://www.broadinstitute.org/igv/) in conjunction with the C. gigas genome (Fang et al. 2012). Associated Publicaiton: XXXXXXX File descriptions: [BiGo_methylation.igv](http://eagle.fish.washington.edu/Mollusk/174gm_analysis/BiGo_methylation.igv) - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [BiGo_igv.xml](http://eagle.fish.washington.edu/Mollusk/174gm_analysis/BiGo_igv.xml) - A session file, which loads methylation and location of C.gigas genome features. Screenshots ![shot](http://eagle.fish.washington.edu/Mollusk/skitch/IGV_19521843.png) ![shot](http://eagle.fish.washington.edu/Mollusk/skitch/IGV_1952187B.png) *** ###_Crassostrea gigas_ high-throughput bisulfite sequencing (sperm and larvae) Citation: Olson, Claire; Roberts, Steven (2014): Crassostrea gigas high-throughput bisulfite sequencing (larvae and sperm tissues). figshare. This fileset contains genomic feature tracks from high-throughput bisulfite sequencing for Pacific oyster (Crassostrea gigas) spermatozoa and larvae samples. Samples were taken from two males (Male 1 and Male 3) and larvae taken from these males at Day 3 (D3) and Day 5 (D5) post-fertilization. Feature tracks were developed to be viewed with Integrative Genomics Viewer (http://www.broadinstitute.org/igv/) in conjunction with the C. gigas genome (Ensembl). Associated Publicaiton: XXXXXXX File descriptions: [methratio_out_CG5x_IGV_M1.igv](http://files.figshare.com/1538436/methratio_out_CG5x_IGV_M1.igv) - Male 1 location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [methratio_out_CG5x_IGV_M3.igv](http://files.figshare.com/1538437/methratio_out_CG5x_IGV_M3.igv) - Male 3 location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [methratio_out_CG5x_IGV_T1D3.igv](http://files.figshare.com/1538440/methratio_out_CG5x_IGV_T1D3.igv) - Larvae from male 1 day 3 post-fertilization location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [methratio_out_CG5x_IGV_T1D5.igv](http://files.figshare.com/1538441/methratio_out_CG5x_IGV_T1D5.igv) - Larvae from male 1 day 5 post-fertilization location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [methratio_out_CG5x_IGV_T3D3.igv](http://files.figshare.com/1538443/methratio_out_CG5x_IGV_T3D3.igv) - Larvae from male 3 day 3 post-fertilization location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [methratio_out_CG5x_IGV_T3D5.igv](http://files.figshare.com/1538444/methratio_out_CG5x_IGV_T3D5.igv) - Larvae from male 3 day 5 post-fertilization location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage. [LarvaeSperm_igv.xml](http://files.figshare.com/1538478/LarvaeSperm_igv.xml) - A session file, which loads sample methylation tracks and location of C.gigas genome features. Screenshots ![shot](http://eagle.fish.washington.edu/Mollusk/skitch/Screenshot_6_18_14_3_50_PM_19524FF7.png) ![shot](http://eagle.fish.washington.edu/Mollusk/skitch/Screenshot_6_18_14_3_27_PM_19524F0D.png)