Schema for Cufflinks Transcripts - D. suzukii Cufflinks Transcripts

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Schema for Cufflinks Transcripts - D. suzukii Cufflinks Transcripts

Database: DsuzGB1 Primary Table: cufflinks_males Row Count: 15,112

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AWUT01013449	`varchar(255)`	values
`chromStart`	243	`int(10) unsigned`	range
`chromEnd`	3624	`int(10) unsigned`	range
`name`	DsuzGB1_CUFF.7.1	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	243	`int(10) unsigned`	range
`thickEnd`	3624	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	3381,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	AWUT01013449	243	3624	DsuzGB1_CUFF.7.1	1000	+	243	3624	0	1	3381,	0,
585	AWUT01013449	8088	58781	DsuzGB1_CUFF.12.2	998	+	8088	58781	0	5	277,611,883,1070,50,	0,352,48577,49518,50643,
585	AWUT01013449	8088	58032	DsuzGB1_CUFF.12.1	996	+	8088	58032	0	6	277,611,630,193,209,166,	0,352,48577,49267,49518,49778,
585	AWUT01013449	55024	63777	DsuzGB1_CUFF.12.3	996	+	55024	63777	0	6	171,634,193,1070,157,198,	0,1641,2331,2582,8248,8555,
585	AWUT01013449	65659	66714	DsuzGB1_CUFF.8.1	998	+	65659	66714	0	2	164,838,	0,217,
585	AWUT01014734	1163	10185	DsuzGB1_CUFF.24.1	1000	+	1163	10185	0	1	9022,	0,
585	AWUT01014734	1163	21099	DsuzGB1_CUFF.23.1	1000	+	1163	21099	0	6	6565,108,199,179,160,2413,	0,15189,16056,16317,16562,17523,
585	AWUT01014734	10251	21099	DsuzGB1_CUFF.23.2	1000	+	10251	21099	0	5	6209,199,179,160,2413,	0,6968,7229,7474,8435,
585	AWUT01015082	3110	4677	DsuzGB1_CUFF.16.1	1000	+	3110	4677	0	1	1567,	0,
585	AWUT01015241	8445	12896	DsuzGB1_CUFF.28.1	998	-	8445	12896	0	4	1146,585,1334,288,	0,1204,1848,4163,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Cufflinks Transcripts (rnaseq_cufflinks) Track Description


	Description This track was created by mapping D. suzukii RNA-Seq reads (generated by the Spotted Wing Drosophila Genome Project) against the D. suzukii DsuzGB1 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 PRJNA221549. References Chiu JC et al. Genome of Drosophila suzukii, the spotted wing drosophila. G3 (Bethesda). 2013 Dec 9;3(12):2257-71. 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.