Day 3-Part I take aways

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