Changes between Version 51 and Version 52 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
08/05/20 10:25:55 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/chip_seq_peaks

    v51 v52  
    2525 * For a detailed explanation on strand cross-correlation analysis see box 2 of this paper ([[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326|Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data ]]).
    2626{{{
    27 /nfs/BaRC_Public/phantompeakqualtools/run_spp.R -c=TreatmentIP.bam -savp=TreatmentIP.spp.pdf -out=TreatmentIP.run_spp.out
     27run_spp.R -c=TreatmentIP.bam -savp=TreatmentIP.spp.pdf -out=TreatmentIP.run_spp.out
    2828}}}
    2929  * ENCODE recommends normalized strand coefficientt (NSC) > 1.05 and relative strand correlation (RSC) > 0.08  [[https://genome.cshlp.org/content/genome/22/9/1813.full.html#boxed-text-3 | Ref]]