CIRCexplorer2 parse parses fusion junction information from results of different aligners to prepare necessary files for following analysis.

Usage and option summary


CIRCexplorer2 parse [options] -t ALIGNER <fusion>


-h --help                      Show help message.
--version                      Show version.
-t ALIGNER                     Aligner (TopHat-Fusion, STAR, MapSplice, BWA, segemehl).
-o OUT --output=OUT            Output directory. [default: circ_out]
--pe                           Parse paired-end alignment file (only for TopHat-Fusion).

Notes about options

  1. CIRCexplorer2 parse could accept results derived from TopHat-Fusion, STAR, MapSplice, BWA and segemehl.
  2. For the alignment parameters of each aligner, some examples have been offered in the tutorial. You could also adjust relevant parameters according to your requirements.
  3. The fusion_junction.bed file has the same format with fusion_junction.bed created by the align module, and would be used by other modules of CIRCexplorer2 to further annotate and characterize circular RNAs.
  4. It will overwrite the output directory automatically, so please be careful when setting the path of output directory.
  5. For paired-end results, you can add --pe option to get more strict fusion reads by considering the mate reads.
  6. For different aligner, the <fusion> is different.
ALigner Fusion file
TopHat-Fusion accepted_hits.bam
STAR Chimeric.out.junction
MapSplice fusions_raw.txt
BWA output sam file
segemehl splicesites.bed


CIRCexplorer2 parse will create a circ_out (you could change output folder using -o) folder, and format and convert relevant fusion information into decent file compatible with CIRCexplorer2.

└── fusion_junction.bed