Schema for Head Tissues TopHat Junctions - Junctions predicted by TopHat using modENCODE RNA-Seq from Head Tissues

Database: DmojImproved Primary Table: head_junctions Row Count: 59,141

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	52145	`int(10) unsigned`	range
`chromEnd`	53233	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	7	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	52145	`int(10) unsigned`	range
`thickEnd`	53233	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	71,70	`longblob`
`chromStarts`	0,1018	`longblob`
`expCount`	52216	`int(10) unsigned`	range
`expIds`	53163	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds
585	improved_6498	52145	53233	JUNC00000001	7	+	52145	53233	0,0,0	2	71,70	0,1018	52216	53163
585	improved_6498	52193	53285	JUNC00000002	1	+	52193	53285	0,0,0	2	23,53	0,1039	52216	53232
585	improved_6498	52204	53219	JUNC00000003	5	+	52204	53219	0,0,0	2	51,56	0,959	52255	53163
585	improved_6498	52244	53234	JUNC00000004	31	+	52244	53234	51,102,255	2	74,71	0,919	52318	53163
585	improved_6498	52396	53186	JUNC00000005	2	+	52396	53186	0,0,0	2	53,23	0,767	52449	53163
585	improved_6498	78362	97988	JUNC00000006	2	+	78362	97988	0,0,0	2	58,33	0,19593	78420	97955
585	improved_6498	80322	80484	JUNC00000007	2	-	80322	80484	0,0,0	2	67,38	0,124	80389	80446
585	improved_6498	98052	98252	JUNC00000008	40	+	98052	98252	51,102,255	2	73,75	0,125	98125	98177
585	improved_6498	98055	98271	JUNC00000009	25	+	98055	98271	51,102,255	2	70,75	0,141	98125	98196
586	improved_6498	207074	213119	JUNC00000010	4	+	207074	213119	0,0,0	2	69,31	0,6014	207143	213088

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

Head Tissues TopHat Junctions (head_junctions) Track Description

Description

This track was created by mapping D. mojavensis RNA-Seq reads from head tissues against the D. mojavensis DmojImproved genome assembly using TopHat2. The RNA-Seq data were generated by modENCODE project and the raw data is available for download at the NCBI Sequence Read Archive (SRA):

Accession number	Description	Platform
SRX017458	Female heads (rep1)	Illumina Genome Analyzer
SRX017459	Female heads (rep2)	Illumina Genome Analyzer II
SRX017460	Male heads (rep1)	Illumina Genome Analyzer
SRX017461	Male heads (rep2)	Illumina Genome Analyzer II

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

Methods

TopHat2 was run against the D. mojavensis genome using the following parameters: -g 1 --b2-very-sensitive --min-intron-length 30 --max-intron-length 150000

References

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

The RNA-Seq data were submitted by the modENCODE project. The original RNA-Seq dataset can be obtained from the NCBI GEO database under the accession number GSE20882.