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Old 02-15-2015, 02:03 AM   #1
wilson90
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Location: Singapore

Join Date: May 2012
Posts: 48
Default Relative STrand Cross-correlation coefficient (RSC) negative value???

Hi All,

I am trying to obtain the RSC value using Phantompeakqualtool on my single-end 50bp ChIP-seq data. No replicate. However, I realize that I am getting a very strange RSC value. It is negative?

Code:
Reading Control tagAlign/BAM file TAC_input.bam 
opened /tmp/RtmpKXlVct/TAC_input.tagAlign16bc12361f946
done. read 1572027 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.06543415 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.173582627089614 
Top 3 estimates for fragment length 0 
Window half size 0 
Phantom peak location 50 
Phantom peak Correlation 0.06434206 
Normalized Strand cross-correlation coefficient (NSC) 2.652784 
Relative Strand cross-correlation Coefficient (RSC) -99.02962 
Phantom Peak Quality Tag NA

My question is how do I intepret this negative value? Can I treat it as 0 since the minimum number of RSC is 0?

Thank you.

Wilson
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