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

Database: DeugGB2 Primary Table: cufflinks_males Row Count: 14,684

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPQ02000031	`varchar(255)`	values
`chromStart`	17154	`int(10) unsigned`	range
`chromEnd`	24035	`int(10) unsigned`	range
`name`	DeugGB2_CUFF.9.1	`varchar(255)`	values
`score`	996	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	17154	`int(10) unsigned`	range
`thickEnd`	24035	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	8	`int(10) unsigned`	range
`blockSizes`	213,757,491,478,271,155,291...	`longblob`
`chromStarts`	0,926,1739,2285,4113,5938,6...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFPQ02000031	17154	24035	DeugGB2_CUFF.9.1	996	+	17154	24035	8	213,757,491,478,271,155,291,378,	0,926,1739,2285,4113,5938,6155,6503,
585	AFPQ02000031	17154	24035	DeugGB2_CUFF.9.2	994	+	17154	24035	10	213,218,160,138,491,478,271,155,291,378,	0,926,1244,1545,1739,2285,4113,5938,6155,6503,
585	AFPQ02000031	17402	24035	DeugGB2_CUFF.9.3	996	+	17402	24035	9	896,160,138,491,478,271,155,291,378,	0,996,1297,1491,2037,3865,5690,5907,6255,
585	AFPQ02000054	2	1557	DeugGB2_CUFF.10.1	1000	+	2	1557	1	1555,	0,
585	AFPQ02000112	2	1014	DeugGB2_CUFF.14.1	1000	+	2	1014	1	1012,	0,
585	AFPQ02000176	19286	20891	DeugGB2_CUFF.25.1	1000	+	19286	20891	1	1605,	0,
585	AFPQ02000256	0	1226	DeugGB2_CUFF.38.1	1000	+	0	1226	1	1226,	0,
585	AFPQ02000256	1666	4018	DeugGB2_CUFF.39.1	1000	+	1666	4018	1	2352,	0,
585	AFPQ02000275	455	1709	DeugGB2_CUFF.41.1	1000	+	455	1709	1	1254,	0,
585	AFPQ02000290	18915	19932	DeugGB2_CUFF.43.1	1000	+	18915	19932	1	1017,	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. eugracilis RNA-Seq reads (generated by the modENCODE project) against the D. eugracilis DeugGB2 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