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.
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