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.
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