Changes between Version 58 and Version 59 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
07/09/21 08:43:24 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/chip_seq_peaks

    v58 v59  
    8484=== [=#repro Step 4: Identify reproducible peaks with the IDR method [for peak-calling experiments with replication]]  ===
    8585
    86 You can identify reproducible peaks with idr function, based on the method of [[https://projecteuclid.org/journals/annals-of-applied-statistics/volume-5/issue-3/Measuring-reproducibility-of-high-throughput-experiments/10.1214/11-AOAS466.full | Qunhua Li et al]] and using [[https://github.com/nboley/idr | code from Nathan Boley]].
     86You can identify reproducible peaks with the 'idr' function, based on the method of [[https://projecteuclid.org/journals/annals-of-applied-statistics/volume-5/issue-3/Measuring-reproducibility-of-high-throughput-experiments/10.1214/11-AOAS466.full | Qunhua Li et al]] and using [[https://github.com/nboley/idr | code from Nathan Boley]].
    8787
    8888Start by running macs2 (macs version 2, not version 1) to call ChIP-seq peaks (see step 3)