Any concise and comprehensive web resource available to learn all about RNA sequencing (RNA-seq) analysis?
Secondly,I am finding quite difficult to find a good review article or original research article describing the analysis of RNA Seq data. Could anyone suggest few?
Thank you in advance.
Look at this biostar thread.
There is a reasonable start using bowtie and R packages here
After that, it'd be good to take a look at the mappers that actually do spliced alignment:
Following alignment, you can look at the various packages to do differential expression analysis:
The tophat and cufflinks are by the same group and tend to be run together. EdgeR and DESeq are R packages in common use.
There are also a number of tools to look for novel splice junctions--including tophat, splicemap, splitseek, and RNAMate/X-Mate. I believe the first 2 are the most commonly used.
Hi Brent, the question you link is about exome sequencing not rna-seq, the tools are similar but there is a difference in the experiment.
I collected some papers on RNA-seq in the respective Mendeley group called RNA-seq. This group was in the beginning slightly biased towards RNA-seq on prokaryotes and differential expression statistics and normalization, but others added eukaryote papers too. Feel free to join. As RNA-seq is pretty much evolving, I wouldn't expect there is a single site or book that is totally comprehensive.
An additional good overview on statistical methods are given by the R packages and resources resulting from simply to query Bioconductor for "rna-seq": http://bioconductor.org/help/search/index.html?q=rna-seq
In addition, here at Bergen University, we held a seminar on Bioinformatics for high-throughput sequencing, here's the curriculum and slides, it is a bit broader in scope than just RNA-seq. There are now possibly many similar university courses out there.
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Michael Dondrup
This thread has a great list of resources related to alternative splicing / isoform identification via RNA-seq.
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Malachi Griffith
This link also gives a firly nice idea on RNA seq data analysis
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Dataminer
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you mean literature or RNA sequence analysis tools?
web based tools with guide
What type of analysis do you want to do? What type of RNA do you want to analylse?
Do you mean RNA sequencing, or RNA sequence analysis? I guess the former.
RNA Sequence Analysis
then the tag is wrong