TopHat2, CuffLinks2 and CummeRbound + GE (SE)
This pipeline uses one of the standard tools in this field, TopHat-cufflinks. It will be useful for the data to analyze first time. For the detection of de novo splicing variants, this pipeline add GO annotations and report high frequent entries.
This pipeline requires reference genome sequences and gene annotation information. First, mapping is performed with TopHat, then using CuffLinks, expression of each gene and each transcript is quantified with new splicing variants detected. The expression level is statistically tested by using CuffDiff, and on the basis of the result, several graphs including clustering of expression pattern are generated by CummeRbund. Finally, GO terms that occur significantly more frequently within each cluster are extracted with GOseq, resulting in visualization using Revigo.
|Species||Human, Rat, Mouse, Drosophila etc.|
|Execution time||About a few days (20M paired-end reads[50bp+50bp])|