Schema for modENCODE Cufflinks Transcripts - D. biarmipes Cufflinks Transcripts from modENCODE RNA-Seq

Database: DbiaGB2 Primary Table: cufflinks_eggs Row Count: 13,460

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFD02000037	`varchar(255)`	values
`chromStart`	2	`int(10) unsigned`	range
`chromEnd`	4236	`int(10) unsigned`	range
`name`	DbiaGB2_CUFF.8.1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	2	`int(10) unsigned`	range
`thickEnd`	4236	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	3186,405,330,	`longblob`
`chromStarts`	0,3439,3904,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFD02000037	2	4236	DbiaGB2_CUFF.8.1	1000	+	2	4236	3	3186,405,330,	0,3439,3904,
585	AFFD02000037	5209	7683	DbiaGB2_CUFF.4.1	1000	+	5209	7683	1	2474,	0,
585	AFFD02000037	6214	7683	DbiaGB2_CUFF.5.1	998	+	6214	7683	2	26,1056,	0,413,
585	AFFD02000037	7754	17841	DbiaGB2_CUFF.53.2	998	+	7754	17841	12	1648,208,72,322,1210,356,462,99,311,283,165,2833,	0,1706,2368,3030,3510,4811,5223,5738,5896,6261,6609,7254,
585	AFFD02000037	7754	14642	DbiaGB2_CUFF.53.1	998	+	7754	14642	10	1648,208,322,1210,356,462,99,311,283,279,	0,1706,3030,3510,4811,5223,5738,5896,6261,6609,
585	AFFD02000079	5	1596	DbiaGB2_CUFF.9.1	1000	+	5	1596	1	1591,	0,
585	AFFD02000085	5440	6535	DbiaGB2_CUFF.11.1	1000	+	5440	6535	1	1095,	0,
585	AFFD02000094	1113	2898	DbiaGB2_CUFF.14.1	1000	+	1113	2898	1	1785,	0,
585	AFFD02000099	3284	4755	DbiaGB2_CUFF.16.1	1000	+	3284	4755	1	1471,	0,
585	AFFD02000099	4856	6233	DbiaGB2_CUFF.15.1	1000	+	4856	6233	1	1377,	0,

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

modENCODE Cufflinks Transcripts (modencode_cufflinks) Track Description


	Description This track was created by mapping D. biarmipes RNA-Seq reads (generated by the modENCODE project) against the D. biarmipes DbiaGB2 assembly. The aligned RNA-Seq reads are then used as input for downstream analysis using Cufflinks. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the BioProject accession number PRJNA63469. References Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23. Trapnell C et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5.

Description