Schema for modENCODE Trinity Transcripts - Transcripts Assembled by Trinity

Database: DbiaGB2 Primary Table: trinity_transcripts Row Count: 57,598

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFD02000037	`varchar(255)`	values
`chromStart`	2	`int(10) unsigned`	range
`chromEnd`	463	`int(10) unsigned`	range
`name`	DbiaGB2_asmbl_5\|m.2	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	4	`int(10) unsigned`	range
`thickEnd`	463	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	461,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFD02000037	2	463	DbiaGB2_asmbl_5\|m.2	1000	+	4	463	1	461,	0,
585	AFFD02000037	466	4145	DbiaGB2_asmbl_9\|m.11	1000	+	468	1695	3	2722,405,239,	0,2975,3440,
585	AFFD02000037	466	4145	DbiaGB2_asmbl_9\|m.12	1000	+	1717	2545	3	2722,405,239,	0,2975,3440,
585	AFFD02000037	466	4145	DbiaGB2_asmbl_9\|m.13	1000	+	3089	3990	3	2722,405,239,	0,2975,3440,
585	AFFD02000037	466	3463	DbiaGB2_asmbl_6\|m.3	1000	+	2234	3461	1	2997,	0,
585	AFFD02000037	466	3463	DbiaGB2_asmbl_6\|m.4	1000	+	1384	2212	1	2997,	0,
585	AFFD02000037	466	3463	DbiaGB2_asmbl_8\|m.10	1000	+	2981	3461	2	441,2492,	0,505,
585	AFFD02000037	466	4145	DbiaGB2_asmbl_7\|m.5	1000	+	468	1695	4	2524,137,405,239,	0,2585,2975,3440,
585	AFFD02000037	466	3463	DbiaGB2_asmbl_8\|m.8	1000	+	1448	2276	2	441,2492,	0,505,
585	AFFD02000037	466	4145	DbiaGB2_asmbl_7\|m.6	1000	+	1717	2545	4	2524,137,405,239,	0,2585,2975,3440,

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

modENCODE Trinity Transcripts (trinity_transcripts) Track Description


	Description Reference-guided and de novo transcripts were assembled by Trinity using D. biarmipes RNA-Seq reads. These assembled transcripts are mapped against the D. biarmipes DbiaGB2 assembly using BLAT. References Grabherr MG et al Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23.

Description