Customize the tools used by ROP

Here we explain how to customize the tools used by ROP.

1. Modify the installation script install.sh to install the tools of interest in the prerequisite_software directory.

2. Please modify rop_commands.sh and replace the corresponding command. During the installation, rop_commands.txt will be created.

For example, in order to use a different aligner to map unmapped reads onto human genome and transcriptome, the following lines need to be modified

echo "$PWD/prerequisite_software/bwa/bwa mem  $PWD/db_human/BWA_version0.6.0/genome.fa" >rop_commands.txt
echo "$PWD/prerequisite_software/bwa/bwa mem  $PWD/db_human/BWA_version0.6.0/isoforms_GRCh38_Ensembl.fasta">>rop_commands.txt