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
CIRCexplorer2 parse
will create a directorycirc_out
by default, and the BED filefusion_junction.bed
under this directory is required for following analysis.- See Parse for detailed information about
CIRCexplorer2 parse
.
For paired-end datas
- TopHat-Fusion
CIRCexplorer2 parse --pe -t TopHat-Fusion tophat_fusion/accepted_hits.bam > CIRCexplorer2_parse.log
Note
CIRCexplorer2 parse
will create a directorycirc_out
by default, and the BED filefusion_junction.bed
under this directory is required for following analysis.- Now
CIRCexplorer2 parse
only support paired-end data aligned by TopHat-Fusion in one step as mentioned in alignment tutorial. - See Parse for detailed information about
CIRCexplorer2 parse
.