Parsing for Circular RNA Fusion Junction Reads

CIRCexplorer2 can parse the alignment results separably rather than together with alignment by CIRCexplorer2 align in one step. In this way, it can support many aligners and support paired-end data.

If you have aligned reads with CIRCexplorer2 align, you could skip this step.

For different aligners

  • TopHat2/TopHat-Fusion
CIRCexplorer2 parse -t TopHat-Fusion tophat_fusion/accepted_hits.bam > CIRCexplorer2_parse.log
  • STAR
CIRCexplorer2 parse -t STAR Chimeric.out.junction > CIRCexplorer2_parse.log
  • MapSplice
CIRCexplorer2 parse -t MapSplice mapsplice_out/fusions_raw.txt > CIRCexplorer2_parse.log
  • BWA
CIRCexplorer2 parse -t BWA RNA_seq_bwa.sam > CIRCexplorer2_parse.log
  • segemehl
CIRCexplorer2 parse -t segemehl splicesites.bed > CIRCexplorer2_parse.log

Note

  1. CIRCexplorer2 parse will create a file back_spliced_junction.bed by default that is required for following analysis.
  2. See Parse for detailed information about CIRCexplorer2 parse.

For paired-end datas

  • STAR
CIRCexplorer2 parse -t STAR Chimeric.out.junction > CIRCexplorer2_parse.log
  • TopHat-Fusion
CIRCexplorer2 parse --pe -t TopHat-Fusion tophat_fusion/accepted_hits.bam > CIRCexplorer2_parse.log

Note

  1. CIRCexplorer2 parse will create a file back_spliced_junction.bed by default that is required for following analysis.
  2. If you use CIRCexplorer2 parse to deal with paired-end data aligned by TopHat-Fusion, please refer to the one step method mentioned in alignment tutorial.
  3. See Parse for detailed information about CIRCexplorer2 parse.