Has Any One Used Cummerbund

Question

[Varun Gupta]

Hi I used cufflinks and generated several transcripts.gtf files for different genes. I found the name of CummeRbund in the manual of Cufflinks. Has anyone used it before. I need to make plots of transcript isoforms or in other words i want to plot my transcripts. Is their anyone who know how to use it or has used it. Any help would be appreciated

Regards Varun

Answer 1

[Nico]

Did you tried it? Just to clarify, it's a Bioconductor package, so it works in R.

As explained on the manual page (http://compbio.mit.edu/cummeRbund/manual.html), it is "is designed to help orgainize and browse the output of a 'cuffdiff' differential expression analysis from Cufflinks".

My impression is that it provides visualisation tools to display differential expression (boxplot, dotplots and so on), rather than "plots of transcripts" (I assume you mean "transcripts displayed with pre-existing annotations", Genome-Browser-like... If you want to get plots similar to the ones on their manual page, then use it. If you want to get GenomeBrowser-like plots, then use something else, depending on what you're most comfortable with, or on what you wish to obtain...