Genome Feature Tracks

Steven Roberts edited this page Feb 27, 2015 · 16 revisions

###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 igv_en

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:
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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;

##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. http://dx.doi.org/10.6084/m9.figshare.749728

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 http://oystergen.es/bigill.

Associated Publicaiton: XXXXXXX

File descriptions:
BiGill_CpG_methylation.igv - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage.

BiGill_exon_clc_rpkm.igv - Exon-specific gene expression values (RPKM) from RNA-seq analysis.

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 - Query (SQLShare) used to derive the methylation feature track from the original methratio output (http://goo.gl/5LGq9Q)

Screenshot
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###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 - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage.

BiGo_igv.xml - A session file, which loads methylation and location of C.gigas genome features.

Screenshots
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###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. http://dx.doi.org/10.6084/m9.figshare.1060465

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 - Male 1 location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage.

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 - 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 - 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 - 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 - 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 - A session file, which loads sample methylation tracks and location of C.gigas genome features.

Screenshots
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