Negative strand shift value in cross-correlation plot (spp peak calling)

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2.6 years ago

varamhcu • 0

enter image description here I am using spp peak caller to extract estimated fragment size and ChIP QC metrics (RSC and NSC values) on my ChIP seq samples. I am using "phantompeakqualtools" for performing the spp peak calling.

Upon performing run_spp.R on the test.bam files I got the following results. I performed with default parameters (A) and (B) Changed the parameter in strand shift (break changed from 5 to 1, Here I am attaching the two plots discussed in question). I observed in plot B the cross-correlation is maximum at a negative value. I couldn't infer the result?

Can anyone help me to understand the need for a negative strand-shift value in peak calling with spp?

Thank you

spp Chris chip-seq peak-calling • 831 views

ADD COMMENT • link 2.5 years ago by varamhcu • 0

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Devon Ryan can you help me to understand this.

ADD REPLY • link 2.5 years ago by varamhcu • 0

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