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.
Command
CIRCexplorer2 annotate -r hg19_ref_all.txt -g hg19.fa -b back_spliced_junction.bed -o circularRNA_known.txt > CIRCexplorer2_annotate.log
Note:
- 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. CIRCexplorer2 annotate
will create a output filecircularRNA_known.txt
containing circRNA informations.- See Annotate for detailed information about
CIRCexplorer2 annotate
.