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).
Notes about options
CIRCexplorer2 parse
could accept results derived from TopHat-Fusion, STAR, MapSplice, BWA and segemehl.- 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.
- The
back_spliced_junction.bed
file has the same format withback_spliced_junction.bed
created by the align module, and would be used by other modules of CIRCexplorer2 to further annotate and characterize circular RNAs. - It will overwrite the output file
back_spliced_junction.bed
directly, so please be careful when setting the path of output directory. - For paired-end results, you can add
--pe
option to get more strict fusion reads by considering the mate reads. - 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