DO NOT USE! DO NOT USE!
This is a program to interpret the results of a MITE-seq experiment. It is an antique version maintained for posterity. Please go here instead: https://github.com/broadinstitute/ORFCall
To install:
Clone repo and type make. This is a very simple, one-source-file project with a two-line handcrafted makefile. You'll need some reasonably modern version of gcc and zlib.
To run:
ORFCall ref.fasta codons_used.dat reads1.fastq [reads2.fastq...]
or
ORFCall -p ref.fasta codons_used.dat reads1a.fastq reads1b.fastq [reads2a.fastq reads2b.fastq...]
The ref.fasta file is a single-contig fasta file describing the amplicon for the MITE-seq experiment. You should mark the open reading frame by delimiting it with square brackets like this:
> my.MITE-seq.ref
TTTGGGCCCAAA[AAGAATAAC]TTTGGGCCCAAA
The codons_used.dat file is a tab-delimited file that starts with a header line enumerating all possible codon sequences. The header must be followed by one line for each codon in the ORF, with the value 0, 1, or 2 for each possible codon sequence. The value 0 means that the planned perturbations do not include the codon. The value 1 indicates that this codon sequence is expected to appear as a planned perturbation. And the value 2 means that this is the wild-type codon sequence.
Like this:
AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA ... TTT
0 1 2 0 1 1 0 0 1 1 0 0 1 0 0 1 1 0
1 0 0 2 0 1 1 0 1 0 1 0 0 1 0 1 1 1
0 2 0 0 1 0 0 1 1 0 0 0 1 1 0 1 0 1
If the fastq files end with ".gz", they will be unzipped on the fly.