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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?
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
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