RNAseq: DEG, eQTL, sQTL, eSNV, ASE where to start?

[LeonDK]

Dear all,

I have a case/control setup on human samples RNA sequenced using an Illumina HiSeq2000, yielding 101bp stranded paired end reads. Preparation was done using Illumina's TruSeq Stranded mRNA Library Prep Kit.

I want to do analyses of
- Differentially Expressed Genes (DEG)
- Expression Quantitative Trait Locus (eQTL)
- Splicing Quantitative Trait Locus (sQTL)
- Expression Single Nucleotide Variant (eSNV)
- Allele Specific expression (ASE)
- Alternative splice isoforms

I have previously worked on DEG, but since I do not have previous experience with the remaining analyses, I am looking for a good read on the matter? A good tutorial explaining the concepts and showing how to perform the analysis, preferably with a working example? (I am fluent in commandline *nix)

Where to start?

[viborilla]

Not sure about manuals/scripts, but I would start reading Lappalainen, et al , Nature 2014 (http://www.nature.com/nature/journal...ATURE-20130926)

The supplementary information are quite complete, although there is no code.

You can find an easy software to do eQTL called fastqtl (http://fastqtl.sourceforge.net/). The publication is still under review, but it is quite easy to use.

For ASE you would check this paper in biorxiv and their software : http://biorxiv.org/content/early/2015/03/05/016097

I hope it helps

[LeonDK]

Okay so I looked extensively around and I found this gem: http://ocw.mit.edu/courses/biology/7...ideo-lectures/

Just for future reference for anyone looking for similar

L