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Old 02-10-2013, 11:51 AM   #1
AgaricX
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Location: Texas

Join Date: May 2012
Posts: 5
Default CummeRbund specify sample order, selecting specific chromosome

Hello community!

I have built a dataset of 30 individuals with varying phenotypes for whom I have complete transcriptome data for a specific tissue. I have piped my data through Tophat->Cufflinks->Cuffdiff and have been looking only at one chromosome (I used Tophat to map to only this chromosome initially).

Obviously, this is not the best way to do this since there may be paralogs on other chromosomes that will map to this one via TopHat. However, I wanted to explore CummeRbund with a small dataset before I pipe through the whole thing (plus I cannot build a SQLite database with the full 30x30 CuffDiff output on only 32GB RAM, but I am rectifying this as we speak).

So, to my questions.

1) Can I SPECIFY THE ORDER of the samples displayed in a graphical output (or exclude certain samples)? I cannot find the proper arguments in the manual, the detailed documentation, or the NatPro article. I basically want csBoxplot and csHeatmap to display the data in a SPECIFIC ORDER since my phenotype is a gradient, and I want the associated expression to be reflected in the figure.

2) Can I build a gene set using getGenes for only one chromosome? I have a largely unannotated genome, so I cannot specify a gene list. For example, I want to store all genes mapped to the X chromosome, and look at expression patterns here (in linear order), compared with individual autosomes (for which I would create a separate gene set).

CuffDiff output row:
XLOC_000016 XLOC_000016 - X:1179960-1213832 q1 q2 OK 9.79622 18.6993 0.932688 -0.0665957 0.946904 1 no

Any suggestions or help would be greatly appreciated. I simply cannot find indications in the literature or documentation on how to do so. Thank you to Loyal, Cole, and the community for a fantastic pipeline!

CummeRbund 2.0.0
Cufflinks 2.0.2

-Brian D.
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