Galaxy | Tool Preview

ChiRA map (version 1.4.30)
Input fasta file
Use single if you have all the transcripts in single fasta file. Use split, if you split the reference into two such that each chimeric read arm corresponds to one of them
Reference fasta file
Second reference fasta file.
Seed length for 1st mapping iteration. bwa-mem parameter -k
Seed length for 2nd mapping iteration. bwa-mem parameter -k
bwa-mem parameter '-T'
bwa-mem parameter '-T'

What it does

This tool handles the mapping of the reads to reference transcriptome. User can choose between the bwa-mem and CLAN alignment tools.