Schema for D. virilis Unmapped Proteins - Assembled Unmapped Proteins from modENCODE D. virilis RNA-Seq

Database: DmojImproved Primary Table: dvir_unmapped_proteins Row Count: 51,792

field	example	SQL type	info
`bin`	587	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	384877	`int(10) unsigned`	range
`chromEnd`	388933	`int(10) unsigned`	range
`name`	Dvir_unmapped_89183_95399	`varchar(255)`	values
`score`	938	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	384877	`int(10) unsigned`	range
`thickEnd`	388933	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	3	`int(10) unsigned`	range
`blockSizes`	11,280,3,	`longblob`
`chromStarts`	0,3384,4053	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
587	improved_6498	384877	388933	Dvir_unmapped_89183_95399	938	-	384877	388933	3	11,280,3,	0,3384,4053
587	improved_6498	386950	387136	Dvir_unmapped_23286_27092	924	-	386950	387136	1	186,	0
587	improved_6498	387121	387509	Dvir_unmapped_22446_69476	845	-	387121	387509	2	64,230,	0,158
587	improved_6498	387518	388086	Dvir_unmapped_3584_75022	919	-	387518	388086	2	326,13,	0,555
587	improved_6498	387623	387836	Dvir_unmapped_59031_45599	885	-	387623	387836	1	213,	0
587	improved_6498	387839	388933	Dvir_unmapped_5593_83119	896	-	387839	388933	2	410,7,	0,1087
587	improved_6498	387956	388211	Dvir_unmapped_18302_24464	902	-	387956	388211	1	255,	0
587	improved_6498	388196	388397	Dvir_unmapped_53075_42452	980	-	388196	388397	1	201,	0
587	improved_6498	388397	388679	Dvir_unmapped_7666_49711	984	-	388397	388679	1	282,	0
587	improved_6498	388550	389623	Dvir_unmapped_39284_76428	919	-	388550	389623	4	163,90,173,3,	0,231,380,1070

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

D. virilis Unmapped Proteins (dvir_unmapped_proteins) Track Description


	Description RNA-seq reads generated by the modENCODE project for D. virilis were mapped against the D. virilis genome using TopHat2. Unmapped reads are collected and assembled using ABySS and CAP3. Coding regions within the assembled unmapped contigs are identified using TransDecoder. This collection of coding regions are aligned against the D. mojavensis genome using tblastn followed by Spaln2. Methods Unmapped RNA-seq reads are partitioned into 1GB chunks and assembled separately using ABySS. The assembled contigs are merged together using CAP3. Candidate coding regions in the collection of assembled D. virilis contigs were identified using TransDecoder using the following parameters: -m 50, --search_pfam Pfam-A.hmm. The collection of predicted D. virilis proteins were initially mapped against the D. mojavensis genome using tblastn to identify regions of similarity. Spaln2 is then used to re-align each protein against their corresponding region with cross-species parameters optimized for D. melanogaster: (-Tdromel -yX -yS). 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. Hass B. TransDecoder (Finding Coding Regions Within Transcripts). Iwata H., and Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln2 that incorporates additional species-specific features. Nucleic Acids Research. 2012, 109 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

Methods

References