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login1$ module load R login1$ R R version 2.1415.03 (20112013-1003-31)01) -- "Security Blanket" Copyright (C) 20112013 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("http://bioconductor.org/biocLite.R") interface to help. Type 'q()' to quit R. > source("http://bioconductor.org/biocLite.R") Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 'lib = "/opt/apps/R/2.15.3/lib64/R/library"' is not writable Would you like to use a personal library instead? (y/n) y Would you like to create a personal library ~/R/x86_64-unknown-linux-gnu-library/2.15 to install packages into? (y/n) y ... > biocLite("DESeq") ... > biocLite("edgeR") ... > q() Save workspace image? [y/n/c]: n |
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- In an actual RNAseq analysis, you might want to trim stray adaptor sequences from your data using a tool like the FASTX-Toolkit, FAR, or cutadapt before aligning.
- You can get a lot more information from RNAseq data than you could from a microarray experiment. You can map transcriptional start sites, areas of unexpected transcription, splice sites, etc. - all because you have full sequence information that we have barely used in this example.
- You can call variants from mapped RNAseq data, just be aware that many regions will have no coverage (because they are not expressed as RNA).
From here...
- Visualize mapped reads in BAM files using IGV to manually check some of the gene counts.
- Look at the more sophisticated "Tuxedo" suite of RNAseq tools, which performs many functions that are especially useful in Eukaryotic genomes.