Galaxy | Tool Preview

ChiRA extract (version 1.4.31)
Selecet Yes if you have an annotation file and provide corresponding genomic fasta file
Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]
Hybrids with less than this score will be discarded in the final output. [0-2.0]
Reference fasta file
Second reference fasta file.
Turning this option on increases the run time of the tool significantly.
IntaRNA --seedBP parameter
IntaRNA --seedMinPu parameter
IntaRNA --accW parameter

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