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

Database: DkikGB2 Primary Table: modencode_tophat Row Count: 94,510

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFH02000026	`varchar(255)`	values
`chromStart`	850	`int(10) unsigned`	range
`chromEnd`	1150	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	4	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	850	`int(10) unsigned`	range
`thickEnd`	1150	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	121,120	`longblob`
`chromStarts`	0,180	`longblob`
`expCount`	971	`int(10) unsigned`	range
`expIds`	1030	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds
585	AFFH02000026	850	1150	JUNC00000001	4	-	850	1150	0,0,0	2	121,120	0,180	971	1030
585	AFFH02000168	334	565	JUNC00000002	16	-	334	565	51,102,255	2	76,104	0,127	410	461
585	AFFH02000219	1625	1817	JUNC00000003	1	+	1625	1817	0,0,0	2	44,56	0,136	1669	1761
585	AFFH02000219	1635	1800	JUNC00000004	1	+	1635	1800	0,0,0	2	34,66	0,99	1669	1734
585	AFFH02000219	1729	1942	JUNC00000005	12	+	1729	1942	51,102,255	2	92,33	0,180	1821	1909
585	AFFH02000219	2051	2295	JUNC00000006	16	+	2051	2295	51,102,255	2	93,96	0,148	2144	2199
585	AFFH02000219	2840	3032	JUNC00000007	1	+	2840	3032	0,0,0	2	81,19	0,173	2921	3013
585	AFFH02000219	2844	3079	JUNC00000008	10	+	2844	3079	51,102,255	2	81,76	0,159	2925	3003
585	AFFH02000219	3210	3471	JUNC00000009	32	+	3210	3471	51,102,255	2	99,97	0,164	3309	3374
585	AFFH02000219	3467	3970	JUNC00000010	5	+	3467	3970	0,0,0	2	89,43	0,460	3556	3927

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. kikkawai RNA-Seq reads (generated by the modENCODE project) against the D. kikkawai DkikGB2 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.