Schema for modENCODE TopHat Junctions - D. bipectinata TopHat Splice Junctions from modENCODE RNA-Seq

Database: DbipGB2 Primary Table: modencode_tophat Row Count: 100,802

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFE02000126	`varchar(255)`	values
`chromStart`	6782	`int(10) unsigned`	range
`chromEnd`	6927	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	6782	`int(10) unsigned`	range
`thickEnd`	6927	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	80,15	`longblob`
`chromStarts`	0,130	`longblob`
`expCount`	6862	`int(10) unsigned`	range
`expIds`	6912	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds
585	AFFE02000126	6782	6927	JUNC00000001	2	+	6782	6927	0,0,0	2	80,15	0,130	6862	6912
585	AFFE02000135	14493	14661	JUNC00000002	1	-	14493	14661	0,0,0	2	38,52	0,116	14531	14609
585	AFFE02000172	2205	19044	JUNC00000003	54	+	2205	19044	34,139,34	2	99,99	0,16740	2304	18945
585	AFFE02000172	18956	19203	JUNC00000004	49	+	18956	19203	51,102,255	2	99,83	0,164	19055	19120
585	AFFE02000172	19276	20691	JUNC00000005	44	+	19276	20691	51,102,255	2	97,97	0,1318	19373	20594
585	AFFE02000172	20795	22537	JUNC00000006	10	+	20795	22537	51,102,255	2	98,77	0,1665	20893	22460
585	AFFE02000172	20797	22554	JUNC00000007	26	+	20797	22554	51,102,255	2	96,97	0,1660	20893	22457
585	AFFE02000172	22664	23805	JUNC00000008	15	+	22664	23805	51,102,255	2	72,99	0,1042	22736	23706
585	AFFE02000172	23743	24653	JUNC00000009	55	+	23743	24653	34,139,34	2	98,96	0,814	23841	24557
585	AFFE02000172	24559	24819	JUNC00000010	68	+	24559	24819	34,139,34	2	99,99	0,161	24658	24720

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

modENCODE TopHat Junctions (modencode_tophat) Track Description

Description

This track was created by mapping D. bipectinata RNA-Seq reads (generated by the modENCODE project) against the D. bipectinata DbipGB2 assembly using Bowtie2 and TopHat. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the BioProject accession number PRJNA63469.

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

Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23.

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