Schema for modENCODE TrueSight Junctions - Junctions predicted by TrueSight using modENCODE RNA-Seq

Database: DmojImproved Primary Table: truesight_junctions Row Count: 92,517

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	52206	`int(10) unsigned`	range
`chromEnd`	53173	`int(10) unsigned`	range
`name`	TrueSight_0	`varchar(255)`	values
`score`	190	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	52206	`int(10) unsigned`	range
`thickEnd`	53173	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	10,10,	`longblob`
`chromStarts`	0,957,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	improved_6498	52206	53173	TrueSight_0	190	+	52206	53173	2	10,10,	0,957,
585	improved_6498	52245	53173	TrueSight_1	781	+	52245	53173	2	10,10,	0,918,
585	improved_6498	52308	53173	TrueSight_2	820	+	52308	53173	2	10,10,	0,855,
585	improved_6498	53288	97965	TrueSight_3	216	+	53288	97965	2	10,10,	0,44667,
585	improved_6498	77766	97965	TrueSight_4	511	+	77766	97965	2	10,10,	0,20189,
585	improved_6498	80379	80456	TrueSight_5	749	+	80379	80456	2	10,10,	0,67,
585	improved_6498	80590	80669	TrueSight_6	667	+	80590	80669	2	10,10,	0,69,
585	improved_6498	98115	98206	TrueSight_7	775	+	98115	98206	2	10,10,	0,81,
585	improved_6498	98115	98229	TrueSight_8	354	+	98115	98229	2	10,10,	0,104,
585	improved_6498	98115	98232	TrueSight_9	554	+	98115	98232	2	10,10,	0,107,

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

modENCODE TrueSight Junctions (truesight_junctions) Track Description

Description

This track was created by mapping D. mojavensis RNA-Seq reads against the D. mojavensis DmojImproved genome assembly using TrueSight. 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
SRX054488 \| SRR166836	Adult females (rep1)	Illumina Genome Analyzer II
SRX054489 \| SRR166837	Adult females (rep2)	Illumina HiSeq 2000
SRX247002 \| SRR768439	Adult males (rep1)	Illumina Genome Analyzer II
SRX247003 \| SRR768440	Adult males (rep2)	Illumina HiSeq 2000

The TrueSight junction predictions from the different libraries are filtered and merged together into a single set of predictions.

Methods

TrueSight was run against the D. mojavensis genome using the following parameters: -i 30 -I 150000.

References

Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J. TrueSight: a new algorithm for splice junction detection using RNA-seq. Nucleic Acids Res. 2013 Feb 1;41(4):e51

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 GSE28078.