Changes between Version 44 and Version 45 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
05/14/18 14:12:13 (7 years ago)
Author:
thiruvil
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/chip_seq_peaks

    v44 v45  
    2727/nfs/BaRC_Public/phantompeakqualtools/run_spp.R -c=TreatmentIP.bam -savp=TreatmentIP.spp.pdf -out=TreatmentIP.run_spp.out
    2828}}}
    29 
     29  * 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]]
    3030  * After this analysis a good ChIP-seq experiment will have a second peak (reflecting the fragment size) at least as tall as the first peak (reflecting read length). This is how the graph should look: ([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/figure/F4/|Fig4E]]). If the second peak is smaller than the first, ([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/figure/F4/|like the example shown in Fig4G Marginal]]),  macs will not estimate fragment size correctly. In that case we recommend running macs with parameters "--nomodel" and "--shiftsize=half_of_the_fragment_size", or "--nomodel" and "--extsize=fragment_size". The fragment size is detected on the strand cross correlation analysis.
    3131