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

Database: DtakGB2 Primary Table: modencode_tophat Row Count: 110,100

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFI02000003	`varchar(255)`	values
`chromStart`	11221	`int(10) unsigned`	range
`chromEnd`	31033	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	1007	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	11221	`int(10) unsigned`	range
`thickEnd`	31033	`int(10) unsigned`	range
`itemRgb`	13118744	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	109,121	`longblob`
`chromStarts`	0,19691	`longblob`
`expCount`	11330	`int(10) unsigned`	range
`expIds`	30912	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds
585	AFFI02000003	11221	31033	JUNC00000001	1007	-	11221	31033	200,45,24	2	109,121	0,19691	11330	30912
585	AFFI02000003	11262	32047	JUNC00000002	5	-	11262	32047	0,0,0	2	68,78	0,20707	11330	31969
585	AFFI02000003	11277	11411	JUNC00000003	1	-	11277	11411	0,0,0	2	53,19	0,115	11330	11392
585	AFFI02000003	30833	30986	JUNC00000004	2	-	30833	30986	0,0,0	2	26,74	0,79	30859	30912
585	AFFI02000003	31056	32092	JUNC00000005	1433	-	31056	32092	200,45,24	2	123,123	0,913	31179	31969
585	AFFI02000003	31058	32420	JUNC00000006	3	-	31058	32420	0,0,0	2	121,36	0,1326	31179	32384
585	AFFI02000003	31105	32176	JUNC00000007	4	-	31105	32176	0,0,0	2	74,51	0,1020	31179	32125
585	AFFI02000003	31969	32249	JUNC00000008	78	-	31969	32249	34,139,34	2	91,124	0,156	32060	32125
585	AFFI02000003	32271	32665	JUNC00000009	2	-	32271	32665	0,0,0	2	61,39	0,355	32332	32626
585	AFFI02000003	32433	32673	JUNC00000010	1	-	32433	32673	0,0,0	2	78,47	0,193	32511	32626

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. takahashii RNA-Seq reads (generated by the modENCODE project) against the D. takahashii DtakGB2 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.