Schema for D. virilis Assembled Transcripts - Assembled Transcripts from modENCODE D. virilis RNA-Seq
  Database: DmojImproved    Primary Table: dvir_asm_transcripts    Row Count: 70,228
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom improved_6498varchar(255) values
chromStart 48500int(10) unsigned range
chromEnd 64738int(10) unsigned range
name Dvir_cfl_males_00023645varchar(255) values
score 538int(10) unsigned range
strand +char(1) values
thickStart 48500int(10) unsigned range
thickEnd 64738int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 12int(10) unsigned range
blockSizes 2,48,14,1,177,39,332,224,3,...longblob  
chromStarts 0,2,51,65,15192,15369,15408...longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585improved_64984850064738Dvir_cfl_males_00023645538+48500647380122,48,14,1,177,39,332,224,3,87,147,2,0,2,51,65,15192,15369,15408,15743,15994,16001,16089,16236,
73improved_6498253001272659Dvir_cfl_females_00001906284+25300127265902235,33,15,15,82,6,64,18,23,2,29,31,21,18,0,31,3,3,17,4,16,3,0,37,70,85,101,184,190,255,273,297,301,330,362,386,404,11749,11781,11785,19618,19635,19639,19655,
587improved_6498309401310377Dvir_cfl_females_00020663584-30940131037706245,358,4,227,63,49,0,246,621,626,861,927,
587improved_6498319459320264Dvir_cfl_females_00011986296+3194593202640322,159,9,112,8,34,7,21,63,15,31,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,162,171,284,292,329,337,358,425,441,472,476,513,535,537,553,554,584,616,630,651,670,683,693,708,718,726,753,759,762,774,
587improved_6498319459320264Dvir_cem_SRR768440_43869_1_3296+3194593202640322,159,9,112,8,34,7,21,63,15,31,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,162,171,284,292,329,337,358,425,441,472,476,513,535,537,553,554,584,616,630,651,670,683,693,708,718,726,753,759,762,774,
587improved_6498319459320264Dvir_cfl_females_00011987296+3194593202640322,159,9,112,8,34,7,21,63,15,31,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,162,171,284,292,329,337,358,425,441,472,476,513,535,537,553,554,584,616,630,651,670,683,693,708,718,726,753,759,762,774,
587improved_6498319459320264Dvir_cfl_males_00013662296+3194593202640322,159,9,112,8,34,7,21,63,15,31,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,162,171,284,292,329,337,358,425,441,472,476,513,535,537,553,554,584,616,630,651,670,683,693,708,718,726,753,759,762,774,
587improved_6498319459320264Dvir_cfl_males_00013661296+3194593202640322,159,9,112,8,34,7,21,63,15,31,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,162,171,284,292,329,337,358,425,441,472,476,513,535,537,553,554,584,616,630,651,670,683,693,708,718,726,753,759,762,774,
587improved_6498319463320264Dvir_cfl_males_00013664298+3194633202640342,1,154,11,110,6,36,4,24,63,6,10,30,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,3,158,169,280,286,325,330,354,418,427,438,468,472,509,531,533,549,550,580,612,626,647,666,679,689,704,714,722,749,755,758,77 ...
587improved_6498319463320264Dvir_cfl_females_00011985298+3194633202640342,1,154,11,110,6,36,4,24,63,6,10,30,4,37,22,2,16,1,29,25,13,21,19,13,8,14,9,8,27,6,3,11,31,0,2,3,158,169,280,286,325,330,354,418,427,438,468,472,509,531,533,549,550,580,612,626,647,666,679,689,704,714,722,749,755,758,77 ...

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

D. virilis Assembled Transcripts (dvir_asm_transcripts) Track Description
 

Description

RNA-seq reads generated by the modENCODE project for D. virilis were mapped against the D. virilis genome using TopHat2 and predicted transcripts are assembled using Cufflinks and CEM. This collection of assembled transcripts are aligned against the D. mojavensis genome using BLASTN and sim4cc.

Methods

The collection of assembled D. virilis transcripts were initially mapped against the D. mojavensis genome using WU-BLASTN to identify regions of similarity. These regions are then re-aligned against the corresponding transcript using sim4cc.

References

Zhou, L., M. Pertea, A. Delcher, L. Florea (2009) Sim4cc: a cross-species spliced alignment program. Nucl. Acids Res. 37(11)

Cufflinks is a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's group at the University of Maryland Center for Bioinformatics and Computational Biology, and Barbara Wold's lab at Caltech.

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.