Schema for modENCODE CEM Transcripts - Transcripts assembled by CEM

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Schema for modENCODE CEM Transcripts - Transcripts assembled by CEM

Database: DmojImproved Primary Table: cem_adult_males Row Count: 22,040

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	385922	`int(10) unsigned`	range
`chromEnd`	428117	`int(10) unsigned`	range
`name`	SRR166834_Pred_156_0_0	`varchar(255)`	values
`score`	998	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	385922	`int(10) unsigned`	range
`thickEnd`	428117	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	6	`int(10) unsigned`	range
`blockSizes`	1263,1434,90,180,82,306,	`longblob`
`chromStarts`	0,1357,2859,3008,41731,41889,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
73	improved_6498	385922	428117	SRR166834_Pred_156_0_0	998	+	385922	428117	0	6	1263,1434,90,180,82,306,	0,1357,2859,3008,41731,41889,
588	improved_6498	401633	402675	SRR166835_Pred_280_0_0	1000	+	401633	402675	0	1	1042,	0,
588	improved_6498	415821	423421	SRR166835_Pred_268_1_2	990	+	415821	423421	0	6	179,153,383,133,138,214,	0,4879,6561,7001,7191,7386,
588	improved_6498	415821	423421	SRR166835_Pred_268_1_1	992	+	415821	423421	0	7	179,151,209,383,133,138,214,	0,4879,5190,6561,7001,7191,7386,
588	improved_6498	421283	423421	SRR166835_Pred_268_1_3	992	+	421283	423421	0	5	228,383,133,138,214,	0,1099,1539,1729,1924,
588	improved_6498	421511	428117	SRR166834_Pred_156_0_4	992	+	421511	428117	0	11	340,661,130,138,281,149,159,163,97,136,306,	0,593,1314,1501,1696,2040,2244,2474,3336,6088,6300,
588	improved_6498	421511	428117	SRR166834_Pred_156_0_3	992	+	421511	428117	0	11	340,661,130,138,257,160,159,163,97,136,306,	0,593,1314,1501,1696,2029,2244,2474,3336,6088,6300,
588	improved_6498	421511	423421	SRR166835_Pred_268_1_4	994	+	421511	423421	0	5	340,661,133,138,214,	0,593,1311,1501,1696,
588	improved_6498	423657	432443	SRR166835_Pred_268_2_5	996	+	423657	432443	0	12	43,159,69,92,136,483,512,342,293,1391,750,198,	0,98,328,1195,3942,4154,4876,5481,5882,6235,7697,8588,
588	improved_6498	428117	430498	SRR166834_Pred_156_1_5	996	+	428117	430498	0	5	177,512,342,282,606,	0,416,1021,1433,1775,

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

modENCODE CEM Transcripts (cemtranscript) 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 GSE28078.