Hi List,

In the edgeR manual it is mentioned that the package may be useful in the 
analysis of other count based studies and I am wondering if the bulk 
segregation studies (based on tag counts) are such a case i.e. hoping for 
advice on the potential rightness or wrongness of doing this...

The general experimental outline is as follows:

>From parents introgressed with DNA containing allelels that are +/- for a 
trait  a set of offspring is generated that segregate for the trait (in my 
case the progeny have been back-crossed to one of the parental lines for 
multiple generations so that they are effectively isogenic backgrounds 
with just the QTL region segregating,  while the parents can have multiple 
regions segregating from the original introgression including the QTL 
region). Offspring are bulked to create pools representing + and - bulks. 
DNA is then isolated from parents and offspring and these are assayed for 
a marker set which is generated as follows:

DNA digested with a restriction enzyme, adaptor ligated to these ends (ie 
tag the restriction digestion sites). Randomly shear DNA and then ligate 
second adaptor. Enrich for fragments with two adaptors and then sequence 
fragments on Illumina HiSeq instrument.  Map tags back to a reference and 
count hits.  We are then looking for reference sequences that are 
differentially hit in the + vs - strains in both parents and offspring. 

My thinking was that parents and offspring are effectively replications of 
the presence or absence of the QTL region and the way the counts are 
obtained has similar sampling properties to when you are doing a DE study 
of gene expression. Hence I thought to use edgeR to do the analysis as it 
can normalise for both overall count numbers and the TMM normalisation for 
target tag complexity and the tagwise implementation can account for the 
technical variance arising from bulking, sampling, mapping efficieny  etc. 


Looking forward to reading your comments.....

Best, Josquin
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