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

Database: DtakGB2 Primary Table: cufflinks_eggs Row Count: 14,973

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFI02000003	`varchar(255)`	values
`chromStart`	10684	`int(10) unsigned`	range
`chromEnd`	32914	`int(10) unsigned`	range
`name`	DtakGB2_CUFF.22.1	`varchar(255)`	values
`score`	998	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	10684	`int(10) unsigned`	range
`thickEnd`	32914	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	646,267,945,	`longblob`
`chromStarts`	0,20228,21285,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFI02000003	10684	32914	DtakGB2_CUFF.22.1	998	-	10684	32914	3	646,267,945,	0,20228,21285,
585	AFFI02000003	35904	37575	DtakGB2_CUFF.26.1	1000	+	35904	37575	1	1671,	0,
585	AFFI02000003	38494	42531	DtakGB2_CUFF.31.1	1000	+	38494	42531	3	647,547,2581,	0,855,1456,
585	AFFI02000003	38567	44782	DtakGB2_CUFF.32.1	1000	+	38567	44782	1	6215,	0,
585	AFFI02000003	39310	42531	DtakGB2_CUFF.31.2	1000	+	39310	42531	2	586,2581,	0,640,
585	AFFI02000004	1	1623	DtakGB2_CUFF.1.1	1000	+	1	1623	1	1622,	0,
585	AFFI02000004	2874	5026	DtakGB2_CUFF.3.1	1000	+	2874	5026	1	2152,	0,
585	AFFI02000004	5871	12614	DtakGB2_CUFF.4.1	1000	+	5871	12614	1	6743,	0,
585	AFFI02000004	14303	16352	DtakGB2_CUFF.6.1	1000	+	14303	16352	1	2049,	0,
585	AFFI02000004	16402	17860	DtakGB2_CUFF.7.1	1000	+	16402	17860	1	1458,	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. takahashii RNA-Seq reads (generated by the modENCODE project) against the D. takahashii DtakGB2 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