NGS Applications
RNA-seq
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Recommendation list
TopHat2, CuffLinks2 and CummeRbund + GE (SE)
TopHat2, CuffLinks2 and CummeRbund + GE (PE)
Trinity, Bowtie, eXpress, DEGseq, clustering and GO analysis (SE)
Trinity, Bowtie, eXpress, DEGseq, clustering and GO analysis (PE)
Trinity, TMAP, eXpress, DEGseq, clustering and GO analysis (SE)
TopHat, HTSeq, DESeq multi samples differentially expressed gene detection analysis (less than 10 N=1 samples)
Related list
cuffdiffOutToHtmlWithChIPpeakAnnotation (for multi comparison, add extra inf from GTF, with link for GE list, max 10 peaks)
BWA DEGSeq multi samples differentially expressed gene detection analysis (PE)
BWA, HTSeq, DESeq multi samples differentially expressed gene detection analysis (PE)
BWA-DEGseq:getGeneExp-DEGseq:FET (PE)
DEGseq:FET for rSeq
DEGseq (FET) for miRNA
FastQC (SE)
rSeq (SE)
Note "SE": For single-end read, "PE": For paired-end read, "GE": Genome explorer which is our original genome browser.
It is necessary to register to analyze your own data.
: The popular pipeline or the latest one that the developer recommend.
Notice: Unrecomend not a tool used by the pipeline but the workflow of the pipelie.