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.