Kou's memo

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Contents

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

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