What it does
This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.
- Tabular file containing CRLs information
- Annotation GTF file
- Reference fasta files. Provide both in case of split reference.
- If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille.
- Tabular file containing chimeras information