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

Database: DrhoGB2 Primary Table: modencode_tophat Row Count: 104,281

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPP02000013	`varchar(255)`	values
`chromStart`	223	`int(10) unsigned`	range
`chromEnd`	676	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	223	`int(10) unsigned`	range
`thickEnd`	676	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	88,12	`longblob`
`chromStarts`	0,441	`longblob`
`expCount`	311	`int(10) unsigned`	range
`expIds`	664	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds
585	AFPP02000013	223	676	JUNC00000001	2	+	223	676	0,0,0	2	88,12	0,441	311	664
585	AFPP02000013	229	741	JUNC00000002	3	+	229	741	0,0,0	2	82,89	0,423	311	652
585	AFPP02000013	258	702	JUNC00000003	1	+	258	702	0,0,0	2	42,50	0,394	300	652
585	AFPP02000013	792	952	JUNC00000004	1	-	792	952	0,0,0	2	75,25	0,135	867	927
585	AFPP02000017	383	616	JUNC00000005	1	+	383	616	0,0,0	2	49,51	0,182	432	565
585	AFPP02000026	54	1057	JUNC00000006	86	+	54	1057	34,139,34	2	96,119	0,884	150	938
585	AFPP02000029	220	1021	JUNC00000007	158	-	220	1021	192,96,154	2	98,98	0,703	318	923
585	AFPP02000030	63	1021	JUNC00000008	36	+	63	1021	51,102,255	2	124,80	0,878	187	941
585	AFPP02000030	254	1024	JUNC00000009	22	+	254	1024	51,102,255	2	110,83	0,687	364	941
585	AFPP02000033	33	224	JUNC00000010	7	-	33	224	0,0,0	2	93,44	0,147	126	180

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. rhopaloa RNA-Seq reads (generated by the modENCODE project) against the D. rhopaloa DrhoGB2 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.