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

Database: DbiaGB2 Primary Table: cufflinks_males Row Count: 15,275

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFD02000037	`varchar(255)`	values
`chromStart`	1738	`int(10) unsigned`	range
`chromEnd`	4104	`int(10) unsigned`	range
`name`	DbiaGB2_CUFF.5.1	`varchar(255)`	values
`score`	996	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	1738	`int(10) unsigned`	range
`thickEnd`	4104	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	4	`int(10) unsigned`	range
`blockSizes`	1252,137,405,198,	`longblob`
`chromStarts`	0,1313,1703,2168,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFD02000037	1738	4104	DbiaGB2_CUFF.5.1	996	+	1738	4104	4	1252,137,405,198,	0,1313,1703,2168,
585	AFFD02000037	4526	16808	DbiaGB2_CUFF.27.1	998	+	4526	16808	12	189,1338,299,208,322,1210,356,614,311,283,165,1800,	0,2101,4577,4934,6258,6738,8039,8451,9124,9489,9837,10482,
585	AFFD02000037	5168	16808	DbiaGB2_CUFF.27.3	998	+	5168	16808	14	854,161,1338,299,208,72,322,1210,356,614,311,283,165,1800,	0,911,1459,3935,4292,4954,5616,6096,7397,7809,8482,8847,9195,9840,
585	AFFD02000037	5168	16808	DbiaGB2_CUFF.27.2	998	+	5168	16808	12	1072,1338,299,208,322,1210,356,614,311,283,165,1800,	0,1459,3935,4292,5616,6096,7397,7809,8482,8847,9195,9840,
585	AFFD02000037	10681	16808	DbiaGB2_CUFF.27.4	998	+	10681	16808	8	425,1210,356,614,311,283,165,1800,	0,583,1884,2296,2969,3334,3682,4327,
585	AFFD02000073	23375	24664	DbiaGB2_CUFF.7.1	1000	+	23375	24664	1	1289,	0,
585	AFFD02000085	538	3021	DbiaGB2_CUFF.8.1	1000	+	538	3021	1	2483,	0,
585	AFFD02000085	3487	10706	DbiaGB2_CUFF.9.1	1000	+	3487	10706	1	7219,	0,
585	AFFD02000099	484	8734	DbiaGB2_CUFF.11.1	1000	+	484	8734	1	8250,	0,
585	AFFD02000099	8934	10373	DbiaGB2_CUFF.10.1	1000	+	8934	10373	1	1439,	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