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

Database: DmojImproved Primary Table: head_cufflinks_adult_males Row Count: 12,736

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	52087	`int(10) unsigned`	range
`chromEnd`	320028	`int(10) unsigned`	range
`name`	TCONS_00000001	`varchar(255)`	values
`score`	992	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	52087	`int(10) unsigned`	range
`thickEnd`	320028	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	7	`int(10) unsigned`	range
`blockSizes`	231,135,170,211,128,169,561,	`longblob`
`chromStarts`	0,1076,45868,129103,161001,...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
73	improved_6498	52087	320028	TCONS_00000001	992	+	52087	320028	7	231,135,170,211,128,169,561,	0,1076,45868,129103,161001,191148,267380,
585	improved_6498	99610	105794	TCONS_00000182	1000	+	99610	105794	1	6184,	0,
585	improved_6498	108179	120896	TCONS_00000184	1000	+	108179	120896	1	12717,	0,
586	improved_6498	206471	217222	TCONS_00000002	1000	+	206471	217222	1	10751,	0,
586	improved_6498	235817	243559	TCONS_00000003	1000	+	235817	243559	1	7742,	0,
586	improved_6498	255335	257911	TCONS_00000186	1000	+	255335	257911	1	2576,	0,
586	improved_6498	258012	260508	TCONS_00000187	1000	+	258012	260508	1	2496,	0,
587	improved_6498	307446	311689	TCONS_00000190	1000	+	307446	311689	1	4243,	0,
587	improved_6498	320165	323074	TCONS_00000191	1000	+	320165	323074	1	2909,	0,
587	improved_6498	344156	346561	TCONS_00000194	1000	+	344156	346561	1	2405,	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