| Cuffdiff is part of the Cufflinks suite. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. 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 produces a number of output files that contain test results for changes in expression at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene. |
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff
| Name | Version | Type | |
|---|---|---|---|
| cufflinks | 2.2.1 | package | |
| cummeRbund | 2.8.2 | package | |
| CUFFDIFF_SCRIPT_PATH | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| find significant changes in transcript expression, splicing, and promoter use | 2.2.1.3 | any | |