Schema for Head Tissues CEM Transcripts - CEM Transcripts using modENCODE RNA-Seq from Head Tissues

Database: DmojImproved Primary Table: head_cem_adult_females Row Count: 9,954

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	52255	`int(10) unsigned`	range
`chromEnd`	319958	`int(10) unsigned`	range
`name`	Head_Dmoj_female_Pred_11_0_1	`varchar(255)`	values
`score`	990	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	52255	`int(10) unsigned`	range
`thickEnd`	319958	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	7	`int(10) unsigned`	range
`blockSizes`	63,135,170,211,128,169,491,	`longblob`
`chromStarts`	0,908,45700,128935,160833,1...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
73	improved_6498	52255	319958	Head_Dmoj_female_Pred_11_0_1	990	+	52255	319958	7	63,135,170,211,128,169,491,	0,908,45700,128935,160833,190980,267212,
73	improved_6498	52318	319958	Head_Dmoj_female_Pred_11_0_2	992	+	52318	319958	7	131,135,170,211,128,169,491,	0,845,45637,128872,160770,190917,267149,
585	improved_6498	79077	80389	Head_Dmoj_female_Pred_44_0_0	1000	+	79077	80389	1	1312,	0,
585	improved_6498	98196	99401	Head_Dmoj_female_Pred_11_1_5	1000	+	98196	99401	1	1205,	0,
585	improved_6498	99602	105883	Head_Dmoj_female_Pred_66_0_0	1000	+	99602	105883	1	6281,	0,
585	improved_6498	108256	120657	Head_Dmoj_female_Pred_70_0_0	1000	+	108256	120657	1	12401,	0,
586	improved_6498	205031	206140	Head_Dmoj_female_Pred_143_0_0	1000	+	205031	206140	1	1109,	0,
73	improved_6498	207143	319958	Head_Dmoj_female_Pred_11_0_4	1000	+	207143	319958	4	3483,128,169,491,	0,5945,36092,112324,
586	improved_6498	224169	226458	Head_Dmoj_female_Pred_151_1_1	1000	+	224169	226458	1	2289,	0,
587	improved_6498	308676	311064	Head_Dmoj_female_Pred_235_0_0	1000	+	308676	311064	1	2388,	0,

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

Head Tissues CEM Transcripts (head_cem_transcript) Track Description


	Description RNA-seq reads generated by the modENCODE project were mapped against the D. mojavensis genome using TopHat2. The aligned RNA-seq reads are assembled together using CEM. References Li W, Jiang T. Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads. Bioinformatics. 2012 Nov 15;28(22):2914-21. The RNA-Seq data were submitted by the modENCODE project. The original RNA-Seq dataset can be obtained from the NCBI GEO database under the accession number GSE20882.

Description