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_females Row Count: 18,861

field	example	SQL type	info
`bin`	73	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	385233	`int(10) unsigned`	range
`chromEnd`	432100	`int(10) unsigned`	range
`name`	SRR166833_Pred_187_0_0	`varchar(255)`	values
`score`	998	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	385233	`int(10) unsigned`	range
`thickEnd`	432100	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	6	`int(10) unsigned`	range
`blockSizes`	1952,1434,90,180,426,746,	`longblob`
`chromStarts`	0,2046,3548,3697,45624,46121,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
73	improved_6498	385233	432100	SRR166833_Pred_187_0_0	998	+	385233	432100	0	6	1952,1434,90,180,426,746,	0,2046,3548,3697,45624,46121,
73	improved_6498	385233	432100	SRR166833_Pred_187_0_1	998	+	385233	432100	0	6	1952,1434,90,180,607,746,	0,2046,3548,3697,45443,46121,
73	improved_6498	386049	432016	SRR166832_Pred_134_0_1	998	-	386049	432016	0	7	1136,1434,90,180,332,129,662,	0,1230,2732,2881,44627,45105,45305,
588	improved_6498	400852	429832	SRR166832_Pred_135_1_1	992	+	400852	429832	0	17	406,179,97,52,228,383,133,138,214,176,159,69,92,136,512,378,293,	0,14969,19848,20316,20431,21530,21970,22160,22355,22672,22903,23133,24000,26747,27681,28250,28687,
588	improved_6498	400852	429832	SRR166832_Pred_135_1_2	992	+	400852	429832	0	18	406,179,97,52,228,383,133,138,214,176,159,69,92,136,483,512,378,293,	0,14969,19848,20316,20431,21530,21970,22160,22355,22672,22903,23133,24000,26747,26959,27681,28250,28687,
588	improved_6498	415898	424828	SRR166833_Pred_187_1_2	994	+	415898	424828	0	10	102,97,52,661,133,138,214,176,159,843,	0,4802,5270,6206,6924,7114,7309,7626,7857,8087,
588	improved_6498	415898	424828	SRR166833_Pred_187_1_3	992	+	415898	424828	0	11	102,97,52,228,383,133,138,214,176,159,843,	0,4802,5270,5385,6484,6924,7114,7309,7626,7857,8087,
588	improved_6498	421013	424828	SRR166833_Pred_187_1_5	994	+	421013	424828	0	8	207,661,133,138,214,176,159,843,	0,1091,1809,1999,2194,2511,2742,2972,
588	improved_6498	421013	424828	SRR166833_Pred_187_1_6	994	+	421013	424828	0	9	207,228,383,133,138,214,176,159,843,	0,270,1369,1809,1999,2194,2511,2742,2972,
588	improved_6498	421511	429832	SRR166832_Pred_135_1_4	994	+	421511	429832	0	14	733,383,133,138,214,176,159,69,92,136,483,512,378,293,	0,871,1311,1501,1696,2013,2244,2474,3341,6088,6300,7022,7591,8028,

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.