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Hello,
I recently came to know about cummeRbund, its amazing and I wanted to use it. I use galaxy tool to map all my sequences using tophat and use cufflinks/cuffdiff for differential expression testing. I can use cuffdiff with a transcript annotation file (.gtf file) along with two bam files (two different conditions). I cannot include more than two bam files and I am just locked up with two conditions per analysis. But in the example of cummeRbund at bioconductor website, a single set of cuffdiff file holds all information about three different samples and I do not have that kind of information with my files. I have six (pairwise) set of cuffdiff files and I do not know how to start my analysis using cummeRbund (I am interested in only six potential pairwise comparisons). Any help would be appreciated!
My another question: Whether isoform tracking file and transcript tracking file are same or different in readcufflinks command?
Thanks,
Gopinath
I recently came to know about cummeRbund, its amazing and I wanted to use it. I use galaxy tool to map all my sequences using tophat and use cufflinks/cuffdiff for differential expression testing. I can use cuffdiff with a transcript annotation file (.gtf file) along with two bam files (two different conditions). I cannot include more than two bam files and I am just locked up with two conditions per analysis. But in the example of cummeRbund at bioconductor website, a single set of cuffdiff file holds all information about three different samples and I do not have that kind of information with my files. I have six (pairwise) set of cuffdiff files and I do not know how to start my analysis using cummeRbund (I am interested in only six potential pairwise comparisons). Any help would be appreciated!
My another question: Whether isoform tracking file and transcript tracking file are same or different in readcufflinks command?
Thanks,
Gopinath