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

Database: DeugGB2 Primary Table: cufflinks_females Row Count: 11,401

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPQ02000031	`varchar(255)`	values
`chromStart`	17227	`int(10) unsigned`	range
`chromEnd`	24072	`int(10) unsigned`	range
`name`	DeugGB2_CUFF.2.1	`varchar(255)`	values
`score`	996	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	17227	`int(10) unsigned`	range
`thickEnd`	24072	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	9	`int(10) unsigned`	range
`blockSizes`	1071,160,138,491,478,271,15...	`longblob`
`chromStarts`	0,1171,1472,1666,2212,4040,...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFPQ02000031	17227	24072	DeugGB2_CUFF.2.1	996	+	17227	24072	9	1071,160,138,491,478,271,155,291,415,	0,1171,1472,1666,2212,4040,5865,6082,6430,
585	AFPQ02000054	6	1601	DeugGB2_CUFF.4.1	1000	+	6	1601	1	1595,	0,
585	AFPQ02000256	2120	3870	DeugGB2_CUFF.24.1	1000	+	2120	3870	1	1750,	0,
585	AFPQ02000534	964	3053	DeugGB2_CUFF.39.1	1000	+	964	3053	1	2089,	0,
585	AFPQ02000547	0	1198	DeugGB2_CUFF.41.1	1000	+	0	1198	1	1198,	0,
585	AFPQ02000613	4291	5874	DeugGB2_CUFF.44.1	1000	+	4291	5874	1	1583,	0,
585	AFPQ02000679	6406	11867	DeugGB2_CUFF.59.1	996	-	6406	11867	3	649,257,140,	0,5004,5321,
585	AFPQ02000679	14701	15706	DeugGB2_CUFF.62.1	1000	+	14701	15706	1	1005,	0,
585	AFPQ02000798	13	1040	DeugGB2_CUFF.57.1	1000	+	13	1040	1	1027,	0,
585	AFPQ02000800	5	1041	DeugGB2_CUFF.58.1	1000	+	5	1041	1	1036,	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