Searching For A Simple Yet Powerful Workflow For Rna-Seq

Question

[Sukhi Singh]

Hi, I have to start working with RNA-Seq data and have worked previously with ChIP-Seq so I am familiar with mapping, coverage, visualizations and tools etc. Could you guys please tell me a simple workflow (published/unpublished) for the analysis of RNA-Seq data, analysing the gene expression between a wild type and knockout sample. I tried rseq, galaxy (which is good) and GENE-Counter, still I am not confident with my analyses and I get lost in the downstream analyses. Could you recommend a good review and pipeline to start with!!

Thanks a lot

Answer 1

[Sameet]

You probably want to look into the following paper. Nature Protocol Paper

[Geparada]

It's a really good review!! ... but instead of Tophat I prefer to use other Cufflinks-compatible mappers, like MapSplice or GSNAP.

[Khader Shameer]

+1 for Cufflinks and MapSplice.

[Geparada]

I fact, now I'm going to try MapSplice 2.0 wich support multi-threads!

[Sukhi Singh]

Is there any major difference b/w MapSplice and Tophat, Also, some people use bwa to map the reads to a custom splicejunction library, I think all of them serve the same purpose, or is there any significant difference b/w them!!

[Sukhi Singh]

Looks good, I am reading it. Thanks

Answer 2

[ngsgene]

This is a well detailed wiki for RNA-Seq analysis

http://seqanswers.com/wiki/How-to/RNASeq_analysis

[Sukhi Singh]

Thanks looks good