Changes between Version 78 and Version 79 of SOPs/atac_Seq

Timestamp:

07/09/21 11:39:30 (4 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -131 +131 @@
 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 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]]. 
-{{{
-idr --samples rep1.narrowPeak rep2.narrowPeak --input-file-type narrowPeak --output-file IDR.txt --plot
-}}}
 
     * If you are working with the nucleosome free region (NFR) ( detail information can be found in the bottom of the page), macs2 BAMPE option also works. When using'BAMPE' option with paired-end reads, we let MACS run the pileup and calculate 'extsize'.
@@ -150 +146 @@
 }}}
  
+
 ==== Other Tools or Options ====
 
@@ -165 +162 @@
                  | grep -P 'chr[\dXY]+[ \t]'  | gzip -nc > ${FILTERED_PEAK}
 
+}}}
+
+=== Subset peaks into reproducible peaks ===
+
+  * 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]]. 
+{{{
+idr --samples rep1.narrowPeak rep2.narrowPeak --input-file-type narrowPeak --output-file IDR.narrowPeak.bed --plot
+}}}
+  * The output file contains the '''scaled IDR value''' (min(int(-125*log2(IDR), 1000)) in the 5th field.  If one wants to choose 0.05 as the IDR threshold to identify "reproducible" peaks, then this metric must be at least 540.
+{{{
+awk '$5 >= 540 {print $0}' IDR.narrowPeak.bed > IDR.narrowPeak.filtered.bed
 }}}