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==September 5== *'''TO DO:''' **Plug in final choices for slopes into Perl code. **Make sure new probe selection algorithm works. **Make sure new scoring works. **Try code out on some sequences. *'''Slope Choices''' **Based on the data in the above PowerPoint presentation, the following slopes were chosen for the code. $m_LLength=18.51978; #Ligation arm length - COSMIC $m_RLength=13.74286; #Extension arm length - COSMIC $m_TLength=-1.89955; #Target length - COSMIC $m_LTm=8.3619; #Ligation Tm - CES22K $m_RTm=-5.3790; #Extension Tm - CES22K $m_LGC=-326.17; #Ligation GC content - COSMIC - Maybe reduce a little if this is too much? $m_RGC=-217.60; #Extension GC content - COSMIC - Maybe reduce a little if this is too much? $m_LUnique=0; #Ignored for now. $m_RUnique=0; #Ignored for now. $g_Offset=268.845; #Offset for Proximal Ligation Base 'G'- Average of COSMIC and CES22K $a_Offset=169.95; #Offset for Proximal Ligation Base 'A'- Average of COSMIC and CES22K $t_Offset=123.78; #Offset for Proximal Ligation Base 'T'- Average of COSMIC and CES22K $c_Offset=180.505; #Offset for Proximal Ligation Base 'C'- Average of COSMIC and CES22K **This data was added to the GetCpgProbes.pl file. *'''Test probe selection algorithm and new scoring system''' **Chromosome 20, being the smallest chromosome, was used for testing (speed purposes). **A section was chosen for selection. ***'''Upload test file, link here''' **The code was tested and debugged.
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