Annotating for Circular RNAs

This step is a clone and integration of CIRCexplorer to make CIRCexplorer2 inherit all the functions from CIRCexplorer. Please see our previous Cell paper for detailed information.


CIRCexplorer2 annotate -r hg19_ref_all.txt -g hg19.fa -b back_spliced_junction.bed -o circularRNA_known.txt > CIRCexplorer2_annotate.log


  1. It will compare back_spliced_junction.bed (See Alignment) and gene annotation file (hg19_ref_all.txt) to determine the boundaries of circular RNAs, and also carries out realignments to fix some mis-alignments.
  2. CIRCexplorer2 annotate will create a output file circularRNA_known.txt containing circRNA informations.
  3. See Annotate for detailed information about CIRCexplorer2 annotate.