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README.md

STAG-CNS

An Order-Aware Conserved Non-coding Sequences (CNS) Discovery Tool For Arbitrary Numbers of Species

Compile the Program

g++ -o stagCNS stagCNS.cpp -std=c++11

Input

The first n ( n = number of sequences) lines contain some additional information about the genes. It contains seven fields separated by space. The fields are gene name, chromosome ID, forward(+)/reverse(-) strand, range of 10kbp upstream, rage of 10kbp downstream respectively. Please check the sample test file (input.fasta).

Run the program

./stagCNS -file fasta_file -mem minimum_CNS_length -out prefix_output_file > out.txt

Example: ./stagCNS -file input.fasta -mem 8 -out TEST > out.txt

Outputs

  1. TEST_CNS_8.csv (contains CNS information)
  2. TEST_MEM_1_8.csv (contains all MEMs)
  3. TEST_MEM_2_8.csv (contains all MEMs without serial number)
  4. TEST_LPMEM_8_csv (contains all CNSs without actual chromosome location )
  5. TEST_MEM_8.html (used for browser visualization )
  6. TEST_LPMEM_8.html (used for browser visualization)
  7. out.txt (contains all console outputs and error logs)

The first file contains the CNS information. The other files are used for visualization.

Visualization

Two ways to visualiza the output

  1. Using XDAT: Run the collowing command on command line

    java -jar xdat.jar

    It will open an window where the TEST_MEM_2_8.csv and TEST_LPMEM_8_csv files can be uploaded (data) to see the visualizations (chart->parallel coordinate set). Don't forget to change the settings (import settings) to accept comma separated files.

  2. Using browser (firefox) Run the following commands:

    firefox TEST_MEM_8.html

    firefox TEST_LPMEM_8.html

  3. Gobe Visualization will be added