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.