For the software, the input data included a long-read sequence dataset with proper annotation, and a short-read sequence tag dataset for the quantification of transcripts. It was applied to the case study of non-target site glyphosate resistance in horseweed and the data was mined to discover resistance target gene(s). Here we presented a software package, CPTRA: C ross- P latform TR anscriptome A nalysis, to analyze transcriptome profiling data from separate methods. The combination of transcriptome data acquisition methods requires cross-platform transcriptome data analysis platforms, including a new software package for data processing. The combination of different next generation sequencing techniques like 454 pyrosequencing and Illumina Genome Analyzer (Solexa) will enable high-throughput and accurate global gene expression profiling in species with limited genome information.
The use of tag-based methods in species without genome sequence should be complemented by other methods such as cDNA library sequencing. However, the transcriptomic analysis with tag-based methods often depends on available genome sequence.
Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performance as compared to other transcriptome analysis platforms including microarrays. Next-generation sequencing techniques enable several novel transcriptome profiling approaches.
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