File: test_PE_normalization.w_base_cov_stats.sh

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#!/bin/bash -ve

if [ ! -e reads.left.fq ]; then
    gunzip -c ../test_DATA/reads.left.fq.gz > reads.left.fq
fi

if [ ! -e reads.right.fq ]; then
    gunzip -c ../test_DATA/reads.right.fq.gz > reads.right.fq
fi

# just for testing purposes, use --max_cov 30 or higher for real applications.
$TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --left reads.left.fq --right reads.right.fq --seqType fq --max_cov 5 --pairs_together --__devel_report_kmer_cov_stats