20160312--complete RNAseq pipeline with reference genome/geneset

todo

for gene annotation, for all analysis

• clusterprofiler, http://bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#kegg-analysis;
• get all information from Uniprot databases;
• get the known gene information;
• write a go function enrichment analysis(can be replaced by clusterprofiler);
• still need a program to extract annotation information;

• extract information(per organism, from ensembl id):
  id mapping information
  protein fasta
  * .dat information for each organism
  GO/KEGG information or other information

• for unknown genome;
  get blastp result
  *generate GO/KEGG annotation from .dat file

ensembl-genebank->uniprot->GO/KEGG->clusterProfiler#enricher

design a differential express gene analysis

• log2(foldchange);
• cufflinks;
• edgeR;