Recommendation list

nAnT-iCAGE (RIKEN CLST)
nAnT-iCAGE (RIKEN CLST) v1.4 TopHat
RECLU ver3.4 (RIKEN CLST)
RECLU ver3.1 (RIKEN CLST)
RECLU: GOAnalysis (RIKEN CLST)
RECLU: PathwayAnalysis (RIKEN CLST)
TopHat2, CuffLinks2 and CummeRbund + GE (SE) for SAGE

Related list

RECLU ver3.0 (RIKEN CLST)

ONLY REGISTERED USERS CAN ANALYZE. CLICK HERE FOR REGISTRATION PROCESS.
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.

References:

• Ohmiya H., Vitezic M., Frith MC., Itoh M., Carninci P., Forrest ARR., Hayashizaki Y., Lassmann T., The FANTOM Consortium (2014) RECLU: a　pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).　BMC Genomics, 15:269, doi: 10.1186/1471-2164-15-269.