An Order-Aware Conserved Non-coding Sequences (CNS) Discovery Tool For Arbitrary Numbers of Species
g++ -o stagCNS stagCNS.cpp -std=c++11
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).
./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
- TEST_CNS_8.csv (contains CNS information)
- TEST_MEM_1_8.csv (contains all MEMs)
- TEST_MEM_2_8.csv (contains all MEMs without serial number)
- TEST_LPMEM_8_csv (contains all CNSs without actual chromosome location )
- TEST_MEM_8.html (used for browser visualization )
- TEST_LPMEM_8.html (used for browser visualization)
- out.txt (contains all console outputs and error logs)
The first file contains the CNS information. The other files are used for visualization.
Two ways to visualiza the output
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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.
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Using browser (firefox) Run the following commands:
firefox TEST_MEM_8.html
firefox TEST_LPMEM_8.html
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Gobe Visualization will be added