Rna-Seq Data Analysis & Good Review/Research Article On Same

Question

[Dataminer]

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.

[Thaman]

you mean literature or RNA sequence analysis tools?

[Dataminer]

web based tools with guide

[Aarons]

What type of analysis do you want to do? What type of RNA do you want to analylse?

[Michael]

Do you mean RNA sequencing, or RNA sequence analysis? I guess the former.

[Dataminer]

RNA Sequence Analysis

[Michael]

then the tag is wrong

Answer 1

[brentp]

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:

• tophat
• splicemap

Following alignment, you can look at the various packages to do differential expression analysis:

• cufflinks
• edgeR
• DESeq

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.

[Michael]

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.

[brentp]

right. but i still think it is a good to refer to from this thread.

Answer 2

[Michael]

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.

Answer 3

[Malachi Griffith]

This thread has a great list of resources related to alternative splicing / isoform identification via RNA-seq.

Answer 4

[Ericc]

I found this site recently, it is very useful!

Answer 5

[Dataminer]

This link also gives a firly nice idea on RNA seq data analysis

http://rna-seqblog.com/