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.
Command
CIRCexplorer2 assemble -r hg19_ref_all.txt circ_out > CIRCexplorer2_assemble.log
Note:
- It will use Cufflinks to assemble circular RNA transcripts with the alignment result (
circ_out/tophat
) of poly(A)−/ribo− RNA-seq (See Alignment). CIRCexplorer2 assemble
will create a directorycufflinks
under thecirc_out
directory by default. All the assembly information of circular RNA transcripts will be created under the directoryannotate
. You could also checkcufflinks.log
file for detailed logs of Cufflinks assembly.- See Assemble for detailed information about
CIRCexplorer2 assemble
.