Schema for TopHat Junctions - D. suzukii TopHat Splice Junctions

Database: DsuzGB1 Primary Table: rnaseq_tophat Row Count: 90,914

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AWUT01012676	`varchar(255)`	values
`chromStart`	13108	`int(10) unsigned`	range
`chromEnd`	13272	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	13108	`int(10) unsigned`	range
`thickEnd`	13272	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	63,37	`longblob`
`chromStarts`	0,127	`longblob`
`expCount`	13171	`int(10) unsigned`	range
`expIds`	13235	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds
585	AWUT01012676	13108	13272	JUNC00000001	1	+	13108	13272	0,0,0	2	63,37	0,127	13171	13235
585	AWUT01012676	21635	21854	JUNC00000002	2	-	21635	21854	0,0,0	2	43,91	0,128	21678	21763
585	AWUT01012676	21989	22243	JUNC00000003	44	-	21989	22243	51,102,255	2	99,93	0,161	22088	22150
585	AWUT01012676	21999	22246	JUNC00000004	140	-	21999	22246	192,96,154	2	98,96	0,151	22097	22150
585	AWUT01012676	22195	44735	JUNC00000005	258	-	22195	44735	192,96,154	2	97,96	0,22444	22292	44639
585	AWUT01012676	22254	33402	JUNC00000006	1	-	22254	33402	0,0,0	2	38,62	0,11086	22292	33340
585	AWUT01012676	40735	44669	JUNC00000007	1	-	40735	44669	0,0,0	2	70,30	0,3904	40805	44639
585	AWUT01013449	8266	8539	JUNC00000008	281	+	8266	8539	192,96,154	2	99,99	0,174	8365	8440
585	AWUT01013449	8307	8536	JUNC00000009	4	+	8307	8536	0,0,0	2	58,73	0,156	8365	8463
585	AWUT01013449	8953	56761	JUNC00000010	268	+	8953	56761	192,96,154	2	98,96	0,47712	9051	56665

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TopHat Junctions (rnaseq_tophat) Track Description

Description

This track was created by mapping D. suzukii RNA-Seq reads (generated by the Spotted Wing Drosophila Genome Project) against the D. suzukii DsuzGB1 assembly using Bowtie2 and TopHat. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the BioProject accession number PRJNA221549.

The TopHat junction predictions from the different libraries are filtered and merged together into a single set of predictions. The predictions are color-coded based on the number of reads supporting the junction:

Color	Number of reads
	> 1000
	500-999
	100-499
	50-99
	10-49
	< 10

References

Chiu JC et al. Genome of Drosophila suzukii, the spotted wing drosophila. G3 (Bethesda). 2013 Dec 9;3(12):2257-71.

Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11.