parse

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

Usage and option summary

Usage:

CIRCexplorer2 parse [options] -t ALIGNER <fusion>

Options:

-h --help                      Show help message.
--version                      Show version.
-t ALIGNER                     Aligner (TopHat-Fusion, STAR, MapSplice, BWA, segemehl).
-b JUNC --bed=JUNC             Output file. [default: back_spliced_junction.bed]
--pe                           Parse paired-end alignment file (only for TopHat-Fusion).
-f                             Statistics fragment numbers rather than read numbers.

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 back_spliced_junction.bed file has the same format with back_spliced_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 file back_spliced_junction.bed directly, 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

Output

CIRCexplorer2 parse will create a back_spliced_junction.bed.

back_spliced_junction.bed