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

Database: DbipGB2 Primary Table: cufflinks_females Row Count: 10,059

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFE02000110	`varchar(255)`	values
`chromStart`	716	`int(10) unsigned`	range
`chromEnd`	1821	`int(10) unsigned`	range
`name`	DbipGB2_CUFF.2.1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	716	`int(10) unsigned`	range
`thickEnd`	1821	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	1105,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFE02000110	716	1821	DbipGB2_CUFF.2.1	1000	+	716	1821	1	1105,	0,
585	AFFE02000126	18	1249	DbipGB2_CUFF.3.1	1000	+	18	1249	1	1231,	0,
585	AFFE02000235	1023	2142	DbipGB2_CUFF.8.1	1000	+	1023	2142	1	1119,	0,
585	AFFE02000235	17991	19175	DbipGB2_CUFF.11.1	1000	+	17991	19175	1	1184,	0,
585	AFFE02000309	66	1328	DbipGB2_CUFF.18.1	998	-	66	1328	2	209,1000,	0,262,
585	AFFE02000339	10236	11677	DbipGB2_CUFF.13.1	1000	+	10236	11677	1	1441,	0,
585	AFFE02000413	2124	6062	DbipGB2_CUFF.24.1	998	-	2124	6062	6	1855,164,438,500,94,404,	0,1909,2133,2635,3195,3534,
585	AFFE02000413	6660	8261	DbipGB2_CUFF.19.1	998	-	6660	8261	2	849,538,	0,1063,
585	AFFE02000413	9808	12152	DbipGB2_CUFF.20.1	1000	-	9808	12152	2	1122,1055,	0,1289,
585	AFFE02000413	12376	16094	DbipGB2_CUFF.28.1	998	+	12376	16094	4	159,494,159,1806,	0,494,1694,1912,

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. bipectinata RNA-Seq reads (generated by the modENCODE project) against the D. bipectinata DbipGB2 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