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==Useful program==

=This program can manage multiple jobs=
in HPC,
~hanada/bin/manage_run.pl

*1.Make command file (to use hpc, you should give full path for any files)
*2.Test how long it takes for each job in command file
*3.login to shaw
*4.Make your directory in /mnt/lustre. in my case-> /mnt/lustre/hanada
Please see https://hpc.msu.edu/twiki/bin/view/Main/ClusterFileSystems in detail

*3.Type"~hanada/bin/manage_run.pl command_file number_of_cpu name_of_your_account time_for_each_job(minutes)"

=This program conducts chi-square test=
in calculon,
~hanada/bin/Chi_test.pl
*1.Make 2*2_file (Category A B C D)
*2.Type"~hanada/bin/Chi_test.pl 2*2_file"
*3.You can get Direction, P value and Q value

=Introduction of software to show network=
http://www.graphviz.org/

==DATA BASE==
=identificatin of cis elements by three algorithms=
Still running in hpc
/mnt/home/hanada/cis_elements/align_ace
In each cluster, I did three runs.

Still running in calculon
/home/hanada/motif/STRESS/mdscan_out
In each cluster, I did 9 runs (7, 8, 9, 10, 11, 12, 13, 14, 15)

Done 
/home/hanada/motif/STRESS/meme_out

Return to Kou's memo.

Retrieved from "http://shiulab.plantbiology.msu.edu/wiki/index.php/Kou%27s_memo"

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