Schema for Head Tissues Cufflinks Transcripts - Cufflinks Transcripts using modENCODE RNA-Seq from Head Tissues

Database: DmojImproved Primary Table: head_cufflinks_adult_females Row Count: 12,561

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	79220	`int(10) unsigned`	range
`chromEnd`	80389	`int(10) unsigned`	range
`name`	TCONS_00000195	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	79220	`int(10) unsigned`	range
`thickEnd`	80389	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	1169,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	improved_6498	79220	80389	TCONS_00000195	1000	+	79220	80389	1	1169,	0,
587	improved_6498	320247	322886	TCONS_00000247	1000	+	320247	322886	1	2639,	0,
587	improved_6498	343936	345158	TCONS_00000250	1000	+	343936	345158	1	1222,	0,
587	improved_6498	345211	346651	TCONS_00000251	1000	+	345211	346651	1	1440,	0,
587	improved_6498	352487	357025	TCONS_00000259	1000	+	352487	357025	1	4538,	0,
587	improved_6498	361020	362715	TCONS_00000264	1000	+	361020	362715	1	1695,	0,
587	improved_6498	362776	364482	TCONS_00000265	1000	+	362776	364482	1	1706,	0,
587	improved_6498	365572	368487	TCONS_00000267	1000	+	365572	368487	1	2915,	0,
587	improved_6498	370732	375063	TCONS_00000269	1000	+	370732	375063	1	4331,	0,
587	improved_6498	376366	378043	TCONS_00000272	1000	+	376366	378043	1	1677,	0,

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

Head Tissues Cufflinks Transcripts (head_cufflinks) Track Description


	Description This track was created by mapping D. mojavensis RNA-seq reads (generated by the modENCODE project) against the D. mojavensis DmojImproved assembly. The aligned RNA-seq reads are then used as input for downstream analysis using Cufflinks. Methods Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. References Cufflinks is a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's group at the University of Maryland Center for Bioinformatics and Computational Biology, and Barbara Wold's lab at Caltech. 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.

Description