Changes between Version 5 and Version 6 of SOPs/InProgressChipSeq


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Timestamp:
05/14/14 15:49:28 (11 years ago)
Author:
ibarrasa
Comment:

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  • SOPs/InProgressChipSeq

    v5 v6  
    1414 * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
    1515=== Step 2: Strand cross correlation analysis ===
    16  * The goal of this step is asses the quality of the IP and an estimate of the fragment size of the DNA immunoprecipitated.
     16 * The goal of this step is to asses the quality of the IP and to estimate the fragment size of the DNA immunoprecipitated.
    1717 * 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 ]]).
    1818{{{
    … …  
    2020}}}
    2121
    22   * After this analysis a good ChIP-seq experiment will have a second peak (reflecting the fragment size) as tall or taller than the first peak (reflecting read length). Example of a good IP. If the second peak is smaller that the first (example of a weak IP) one macs will not estimate fragment size correctly. In that case we recommend running macs with parameters "--nomodel" and "--shiftsize=half_of_the_fragment_size". The fragment size is detected on the strand cross correlation analysis.
     22  * 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 that 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". The fragment size is detected on the strand cross correlation analysis.
    2323 
    2424=== Step 3: Call peaks (bound regions) ===