Cuffdiff manual

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Cuffdiff takes a GTF2/GFF3 file of transcripts as input, along with two or more SAM files containing the fragment alignments for two or more samples. It CummeRbund begins by re-organizing output files of a cuffdiff analysis, and storing these data in a For detailed file structure see cufflinks manual.For detailed file structure see cufflinks manual. Four .diff files are created: • isoform exp.diff Transcript differential FPKM. I've installed cummerbund and read the manual of cummerbund and cuffdiff but I want to know the biological meaning of the diff file. Given GTF and BAM files, Cuffdiff performs differential expression analysis of genes and transcripts using the Cufflinks algorithm. To use replicate samples Cuffdiff is a highly accurate tool for performing these comparisons, and can tell you not only which genes are up- or down-regulated between two or more