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

Database: DeugGB2 Primary Table: cufflinks_eggs Row Count: 18,245

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPQ02000007	`varchar(255)`	values
`chromStart`	21	`int(10) unsigned`	range
`chromEnd`	1127	`int(10) unsigned`	range
`name`	DeugGB2_CUFF.2.1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	21	`int(10) unsigned`	range
`thickEnd`	1127	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	1106,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFPQ02000007	21	1127	DeugGB2_CUFF.2.1	1000	+	21	1127	1	1106,	0,
585	AFPQ02000009	3	1056	DeugGB2_CUFF.4.1	1000	+	3	1056	1	1053,	0,
585	AFPQ02000010	4	1173	DeugGB2_CUFF.6.1	1000	+	4	1173	1	1169,	0,
585	AFPQ02000014	24	1125	DeugGB2_CUFF.5.1	1000	+	24	1125	1	1101,	0,
585	AFPQ02000015	6	1015	DeugGB2_CUFF.7.1	1000	+	6	1015	1	1009,	0,
585	AFPQ02000018	388	1849	DeugGB2_CUFF.8.1	1000	+	388	1849	1	1461,	0,
585	AFPQ02000025	11	1107	DeugGB2_CUFF.9.1	1000	+	11	1107	1	1096,	0,
585	AFPQ02000031	2727	12479	DeugGB2_CUFF.13.1	1000	+	2727	12479	1	9752,	0,
585	AFPQ02000031	12557	13691	DeugGB2_CUFF.12.1	1000	+	12557	13691	1	1134,	0,
585	AFPQ02000031	17560	23748	DeugGB2_CUFF.96.1	994	+	17560	23748	9	738,160,138,491,478,271,155,291,91,	0,838,1139,1333,1879,3707,5532,5749,6097,

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