- Tuxedo pipeline is useful for
- Identifying novel transcripts and genes in our samples.
- Identifying changes in these novel transcripts and genes between conditions.
- Identify differential expression as well as differntial regulation.
- It can also be run in a mode to ignore novel events.
- The pipeline has 5 steps that we have covered (for novel):
- tophat - mapping
- cufflinks - transcript assembly
- cuffmerge - merge assembly across samples and compare to annotated transcripts
- cuffquant - quantify expression values so cuffdiff doesnt have to do that step
- cuffdiff - differential expression analysis
- The pipeline has 2 that we have covered (without novel):
- tophat - mapping
- cuffdiff - differential expression analysis
- Most of the outputs are tab delimited files, so unix commands come in handy for parsing and getting meaningful answers from our tuxedo pipeline.
- Some simple downstream analysis can be
- making plots using cummeRbund, by reading in cuffdiff results as an R object.
- Moving your bam files to your own computer to view them on a genome browser like IGV
- Identify enriched GO terms using GOSeq
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