De Novo Assembly for Circular RNA Transcripts

CIRCexplorer2 employs Cufflinks to carry out de novo assembly for circular RNA transcripts, and charaterizes alternative splicing based on the assembled results. So it is the key step before analyzing the landscape of alternative back-splicing and alternative splicing of circular RNAs.


CIRCexplorer2 assemble -r hg19_ref_all.txt circ_out > CIRCexplorer2_assemble.log


  1. It will use Cufflinks to assemble circular RNA transcripts with the alignment result (circ_out/tophat) of poly(A)−/ribo− RNA-seq (See Alignment).
  2. CIRCexplorer2 assemble will create a directory cufflinks under the circ_out directory by default. All the assembly information of circular RNA transcripts will be created under the directory annotate. You could also check cufflinks.log file for detailed logs of Cufflinks assembly.
  3. See Assemble for detailed information about CIRCexplorer2 assemble.