Schema for Unmapped modENCODE RNA-Seq - Assembled Unmapped modENCODE RNA-Seq Reads

Database: DmojImproved Primary Table: SRR166834_unmapped Row Count: 107,263

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	804	`int(10) unsigned`	range
`chromEnd`	912	`int(10) unsigned`	range
`name`	SRR166834_unmapped_96833	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	804	`int(10) unsigned`	range
`thickEnd`	912	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	108,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
585	improved_6498	804	912	SRR166834_unmapped_96833	1000	-	804	912	1	108,	0,
585	improved_6498	5032	5107	SRR166834_unmapped_78727	1000	+	5032	5107	1	75,	0,
585	improved_6498	10358	10466	SRR166834_unmapped_96833	1000	-	10358	10466	1	108,	0,
585	improved_6498	15109	15217	SRR166834_unmapped_96833	1000	-	15109	15217	1	108,	0,
585	improved_6498	52291	98018	SRR166834_unmapped_99469	992	-	52291	98018	3	27,136,66,	0,872,45661,
585	improved_6498	56431	56485	SRR166834_unmapped_96075	1000	+	56431	56485	1	54,	0,
585	improved_6498	63516	64173	SRR166834_unmapped_52894	998	-	63516	64173	1	657,	0,
585	improved_6498	64149	64283	SRR166834_unmapped_96906	956	+	64149	64283	2	94,40,	0,94,
585	improved_6498	64261	64353	SRR166834_unmapped_41125	1000	+	64261	64353	1	92,	0,
585	improved_6498	77330	77405	SRR166834_unmapped_34188	1000	+	77330	77405	1	75,	0,

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

Unmapped modENCODE RNA-Seq (unmapped_rnaseq) Track Description


	Description RNA-seq reads generated by the modENCODE project for D. mojavensis were mapped against the D. mojavensis genome using TopHat2. Unmapped reads are collected and assembled using ABySS and CAP3. The assembled unmapped reads are then mapped against the D. mojavensis genome using BLAT. Methods Unmapped RNA-seq reads are partitioned into 1GB chunks and assembled separately using ABySS. The assembled contigs are merged together using CAP3. References Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009 Jun;19(6):1117-23. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999 Sep;9(9):868-77. 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.

Description