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.
Inputs
- A fasta file containing reads
- A reference fasta file containing transcript sequences
- An optional second reference fasta file, incase if you split your reference into two
Output
- BED file containing the alignments
- unmapped FASTA file (only for aligner BWA-MEM)