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#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Process_cmd;
my $usage = "usage: $0 Trinity.fasta reads.fa\n\n";
my $trin_fa = $ARGV[0] or die $usage;
my $reads_fa = $ARGV[1] or die $usage;
main: {
my $salmon_index = "$trin_fa.salmon.idx";
my $cmd = "salmon --no-version-check index -t $trin_fa -i $salmon_index --type quasi -k 25 -p 1";
&process_cmd($cmd);
$cmd = "salmon --no-version-check quant -i $salmon_index -l U -r $reads_fa -o salmon_outdir -p 1 --minAssignedFrags 1 ";
&process_cmd($cmd);
exit(0);
}
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