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

Database: DkikGB2 Primary Table: cufflinks_males Row Count: 12,672

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFH02000335	`varchar(255)`	values
`chromStart`	48497	`int(10) unsigned`	range
`chromEnd`	58968	`int(10) unsigned`	range
`name`	DkikGB2_CUFF.11.1	`varchar(255)`	values
`score`	998	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	48497	`int(10) unsigned`	range
`thickEnd`	58968	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	4	`int(10) unsigned`	range
`blockSizes`	500,549,185,853,	`longblob`
`chromStarts`	0,563,1171,9618,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	AFFH02000335	48497	58968	DkikGB2_CUFF.11.1	998	+	48497	58968	4	500,549,185,853,	0,563,1171,9618,
585	AFFH02000335	52817	55711	DkikGB2_CUFF.14.1	1000	+	52817	55711	1	2894,	0,
585	AFFH02000335	52817	55711	DkikGB2_CUFF.12.1	1000	+	52817	55711	2	2117,687,	0,2207,
585	AFFH02000335	59998	61639	DkikGB2_CUFF.10.2	996	+	59998	61639	3	642,155,696,	0,702,945,
585	AFFH02000335	59998	61639	DkikGB2_CUFF.10.1	996	+	59998	61639	4	642,155,627,11,	0,702,945,1630,
585	AFFH02000335	63258	68468	DkikGB2_CUFF.15.1	998	+	63258	68468	5	223,710,507,144,979,	0,1602,2379,4026,4231,
585	AFFH02000335	64100	68468	DkikGB2_CUFF.15.2	998	+	64100	68468	5	296,710,507,144,979,	0,760,1537,3184,3389,
585	AFFH02000335	70883	72877	DkikGB2_CUFF.13.1	998	+	70883	72877	2	787,1149,	0,845,
585	AFFH02000335	76222	84694	DkikGB2_CUFF.18.1	998	-	76222	84694	5	921,967,176,275,418,	0,1514,4618,7502,8054,
585	AFFH02000335	84813	90236	DkikGB2_CUFF.21.2	1000	+	84813	90236	4	1963,1400,432,576,	0,2892,4354,4847,

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. kikkawai RNA-Seq reads (generated by the modENCODE project) against the D. kikkawai DkikGB2 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