Human Transcriptome RNA-Seq Analysis Using MacVector

With MacVector Pro and Assembler you can use Bowtie to perform RNA-Seq analyses using NGS data. The interface even has specialized output tabs listing the coverage information and statistics for each annotated CDS and gene feature on the genome. There is an example tutorial in the /Applications/MacVector/Documentation folder called “RNASeq Expression Analysis Tutorial.pdf” that illustrate the analysis using a small (1.6 Mbp) prokaryotic genome.

What surprises many people is that the combination of MacVector and modest Macintosh hardware can actually perform this analysis on the human genome. Now there are limitations to this – it’s not currently practical to do this with the entire genome due to memory and processing constraints, but it is possible to run an analysis against the known Human Transcriptome. The latest version of this can be downloaded from the GENCODE database. There is a new RNA-Seq Human Transcriptome Analysis Tutorial that describes the basic procedure in detail and some sample data that can be downloaded. The end result is that you get a table similar to that shown below that can be copied and pasted into Microsoft Excel for additional analysis.

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