1. Run ./autogen.sh if you cloned from GitHub (This step is not required if you downloaded source code from release page.)
2. Run ./configure --disable-shared
3. Run make
4. Run sudo make install if you want to install globally
   • Copy src/matataki, src/matataki-builddb, src/refseqextract to your directory that is contained in PATH variable.

WARNING: building index requires around 30 GB RAM. We recommend to use pre-built index files to quantify human and mouse

1. Download RefSeq FASTA formatted RNA Sequences from NCBI. (For example, ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.1.rna.fna.gz)
2. Download refseq2gene from NCBI.
3. Extract and clean sequences from RefSeq.
   • Run refseqextract -o OUTPUT_FASTA -t TAXID GENE2REFSEQ REFSEQ_FASTA...
   • For example, run refseqextract -o clean-mouse.fna.gz -t 10090 gene2refseq.gz *.rna.fna.gz to create a mouse RNA sequence FASTA.
4. Run matataki-builddb -m -n 32 GENE2REFSEQ REFSEQ_FASTA DBFILE to build index file.
   • For example, run matataki-builddb -m -n 32 gene2refseq.gz clean-mouse.fna.gz mouse-32.idx to build a mouse index file.

This step is required only once for each species.

1. Prepare RNA-Seq FASTQ file.
2. Run matataki -o OUTPUT INDEXDB FASTQ [FASTQ]

• For example, run matataki -o result.txt mouse-32.idx SEQUENCES.fastq

• Matataki can read and write gzip or bzip2 compressed file transparently.

GNU General Public License version 3 or later

Copyright (C) 2016 OKAMURA, Yasunobu Copyright (C) 2009-2011 FAL Labs (kyoto cabinet)