Hi,
I have been preparing cufflinks transcript.gtf files from mutant vs. wildtype strains of mice in order to do differential expression analysis. We have replicate samples from each. After cufflinks was run for each sample, I merge the gtf files with cuffmerge --as specified by the online documentation (http://cufflinks.cbcb.umd.edu/tutorial.html, "Differential analysis").
To run cuffdiff, only one gtf file argument is accepted, along with multiple bam files for each condition, and replicate. Are the cufflinks results from wildtype and mutant supposed to be combined into a single gtf file?
Joe
I have been preparing cufflinks transcript.gtf files from mutant vs. wildtype strains of mice in order to do differential expression analysis. We have replicate samples from each. After cufflinks was run for each sample, I merge the gtf files with cuffmerge --as specified by the online documentation (http://cufflinks.cbcb.umd.edu/tutorial.html, "Differential analysis").
To run cuffdiff, only one gtf file argument is accepted, along with multiple bam files for each condition, and replicate. Are the cufflinks results from wildtype and mutant supposed to be combined into a single gtf file?
Joe
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