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SegSeq RELEASE NOTES 1.0.0

Dec 22 2008

http://www.broad.mit.edu/cancer/pub/solexa_copy_numbers/


INTRODUCTION

This release contains the Matlab source code to detect copy-number
alterations from the aligned positions of short sequence reads.


PREREQUISITES

*  Matlab 7.5 or higher


INSTALLATION

1) Create a directory for the Matlab source code and auxiliary files

2) Download the following archive files from the above website into
   the new directory

*  arachne_qltout_marks.tar.gz            (Example cell line datasets)
*  SegSeq_1.0.0_matlab.tar.gz             (Matlab source code)
*  hg18_alignable_N36_D2.tar.gz           (Matlab files with sample alignable
                                          genome calculations)

3) Extract each of the above archive files
tar xvf arachne_qltout_marks.tar.gz
tar xvf SegSeq_1.0.0_matlab.tar.gz
tar xvf hg18_alignable_N36_D2.tar.gz

4) Launch Matlab

5) Run SeqSeg with the example cell line dataset (NCI-H2347):

*  SegSeq -i H2347_BL2347_solexa_sampleinfo.txt -s H2347 [Optional params]

Refer to the README.txt file for more information about the optional
parameters to SegSeq


CHANGE LOG
