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NAMS walkthrough example

Below is the step by step instruction on how to install and run stand-alone NAMS on a x86_64 Linux/Unix server. For more details please refer to README file in the package.

Install NAMS

  1. Download the NAMS stand-alone package here or use the following command:

        $ wget http://sunlab.cpy.cuhk.edu.hk/NAMS/data/NAMS-latest.tar.gz

  2. Uncompress the package:

        $ tar zxf NAMS-latest.tar.gz

  3. A sub-directory named NAMS-latest will be created. All the required programs and data are included in this directory.

  4. Change to this directory:

        $ cd NAMS-latest

Run NAMS

In order to facilitate the process, we have provided a test dataset which contains a sub-list of transcripts in the stand-alone package under the testing_dataset/ directory.

To run NAMS on this testing dataset:

        $ ./run_testing_dataset.sh

The output should be like:

This script is used to demonstrate how to run NAMS on the test datasets.
There are two test datasets: "TAIR10.ncRNA.fa" and "TAIR10.mRNA.fa" both under the "testing_dataset" directory.

Run NAMS on the "TAIR10.ncRNA.fa":
Command line: ./NAMS testing_dataset/TAIR10.ncRNA.fa testing_dataset TAIR10.ncRNA
***** WARNING: Directory testing_dataset exists! *****
========== NAMS start: Mon Aug 12 13:33:41 HKT 2019 ==========
Step 1: Size filter
Step 2: ORF filter
Step 3: Homolog filter
Step 4: Publish results.
========== NAMS end:   Mon Aug 12 13:52:04 HKT 2019 ==========
The Output files are "testing_dataset/TAIR10.ncRNA.classification" and "testing_dataset/TAIR10.ncRNA.stat".

Run NAMS on the "TAIR10.mRNA.fa":
Command line: ./NAMS testing_dataset/TAIR10.mRNA.fa testing_dataset TAIR10.mRNA
***** WARNING: Directory testing_dataset exists! *****
========== NAMS start: Mon Aug 12 13:52:04 HKT 2019 ==========
Step 1: Size filter
Step 2: ORF filter
Step 3: Homolog filter
Step 4: Publish results.
========== NAMS end:   Mon Aug 12 14:04:22 HKT 2019 ==========
The Output files are "testing_dataset/TAIR10.mRNA.classification" and "testing_dataset/TAIR10.mRNA.stat".

This testing dataset contains 500 coding transcripts and 500 non-coding transcripts obtained from the TAIR project. Please refer to README file for more information on how to run NAMS.


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