Changes between Version 71 and Version 72 of SOPs/atac_Seq

Timestamp:

07/09/21 08:35:08 (4 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -128 +128 @@
 macs2 callpeak -t foo_tn5_pe.bed -n foo -f BED -g mm -q 0.01 --nomodel --shift -75 --extsize 150 --call-summits --keep-dup all
 }}}
-       * If you have biological replicates, you can identify reproducible peaks with idr function ( [[http://barcwiki.wi.mit.edu/wiki/SOPs/chip_seq_peaks#repro | Detail information]] )
+       * If you have biological replicates, you can identify reproducible peaks with idr function ( [[http://barcwiki.wi.mit.edu/wiki/SOPs/chip_seq_peaks#repro | Detail information]]), 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]]. 
 {{{
 idr --samples rep1.narrowPeak rep2.narrowPeak --input-file-type narrowPeak --output-file IDR.txt --plot