Changes between Version 36 and Version 37 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
10/07/16 09:08:37 (8 years ago)
Author:
gbell
Comment:

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  • SOPs/chip_seq_peaks

    v36 v37  
    33 
    44=== Basic Approach ===
    5  * For each sample map the reads to the appropriate genome (eg.using Bowtie2).
     5 * For each sample map the reads to the appropriate genome (e.g. with Bowtie2).
    66 * Call peaks (eg. MACS).  Peaks can be called without control, however, it's highly recommended a control was used in the experimental design, eg. IgG or input, input is preferred over IgG.
    7  * Note that quality control is important after read mapping and after peak calling.  The ENCODE consortium recommends some [[https://genome.ucsc.edu/ENCODE/qualityMetrics.html quality metrics]].
     7 * Note that quality control is important after read mapping and after peak calling.  The ENCODE consortium recommends some [[https://genome.ucsc.edu/ENCODE/qualityMetrics.html|quality metrics]].
    88
    99=== Reviews ===
    … …  
    1111
    1212[[http://nar.oxfordjournals.org/content/early/2010/11/25/nar.gkq1187.abstract?etoc|A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs]] (NAR Nov. 2010)
     13
     14[[https://www.encodeproject.org/documents/108d2515-c053-4b18-bc65-27e8f26d62c5/@@download/attachment/MethylC-SeqStandards_ENCODE3_EM.pdf|ENCODE and modENCODE Guidelines For Experiments Generating ChIP [...] Genome Wide Location Data]]
    1315
    1416=== Step 1: Map reads ===