Changes between Version 84 and Version 85 of SOPs/atac_Seq


Ignore:
Timestamp:
07/09/21 14:14:06 (4 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/atac_Seq

    v84 v85  
    183183 *  [[https://github.com/jsh58/Genrich | Genrich]]
    184184
    185 ==== Subset peaks into reproducible peaks ====
     185=== Subset peaks into reproducible peaks ===
    186186
    187187  * If you have biological replicates, you 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]].
    … …  
    194194}}}
    195195
    196   * To convert the 'scaled IDR value' into the actual IDR (somewhat analogous to the FDR), the formula is 2^scaled_IDR_value/(-125)
     196  * To convert the 'scaled IDR value' into the actual IDR (somewhat analogous to the FDR), the formula is 2^scaled_IDR_value/(-125)^ , although scaled IDR values of 1000 (the max value) have an IDR < 0.004.
    197197
    198198=== [=#AfterPeakQC Quality control after calling peaks] ===