Changes between Version 55 and Version 56 of SOPs/chip_seq_peaks

Timestamp:

08/07/20 07:49:05 (4 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -162 +162 @@
 === [=#repro Step 4 [for peak-calling experiments with replication]: Identify reproducible peaks] ===
 
-For more information about the method, see the main [[https://sites.google.com/site/anshulkundaje/projects/idr| IDR page]].
+For more information about the method, see the main [[https://github.com/nboley/idr | IDR page]].
 
 Run macs2 (macs version 2, not version 1) to call ChIP-seq peaks (see step 3)
@@ -179 +179 @@
 ==== Estimate Irreproducibility Discovery Rate (IDR) between replicates ====
 
-The interface of this command has been slightly modified by BaRC, but the main method remains exactly the same.  The modified scripts are in /nfs/BaRC_Public/BaRC_code/R/IDR
-
-The command requires names and lengths of all chromosomes in a file (ex: chromInfo) of format chromosome<tab>size.
-
-{{{
-# USAGE: batch-consistency-analysis.r [peakfile1] [peakfile2] [peak.half.width] [outfile.prefix] [min.overlap.ratio] [is.broadpeak] [ranking.measure]\
-#
-# peak.half.width => set the peak.half.width to the reported peak width in the peak files (-1 (minus one) is recommended)
-# outfile.prefix => the one-word name of your analysis
-# min.overlap.ratio => fractional bp overlap (0 to 1) between peaks in replicates to be considered as overlapping peaks. (0 is recommended)  
-# is.broadpeak => Is the peak file format broadPeak (or else is narrowPeak)? (F for false)  The IDR method is not recommended for broad peaks.
-# ranking.measure => p.value is recommended
-
-batch-consistency-analysis.r IP.1_vs_control.1.regionPeak.gz IP.2_vs_control.2.regionPeak.gz -1 rep1_vs_rep2_IDR 0 F p.value chromInfo.txt 
-}}}
-
-==== Create the IDR plots ====
-{{{
-# USAGE: batch-consistency-plot.r [npairs] [output.prefix] [input.file.prefix1] [input.file.prefix2] [input.file.prefix3] ....
-# This method can plot 1 or more pairs of replicates
-
-batch-consistency-plot.r 1 rep1_vs_rep2_IDR_plot rep1_vs_rep2_IDR
-}}}
-
-==== Generate a conservative and an optimal final set of peak calls ==== 
-{{{
-# Use an IDR cutoff of 0.01 to 0.05, depending on the number of pre-IDR peaks and size of the genome:
-# IDR <= 0.05 for < 100K pre-IDR peaks for large genomes (human/mouse)
-# IDR <= 0.01 or 0.02 for ~15K to 40K peaks in smaller genomes such as worm
-# awk note: $NF refers to the last data column which (in the *overlapped-peaks.txt file) is the IDR
-
-awk '{ if($NF < 0.05) print $0 }' rep1_vs_rep2_IDR-overlapped-peaks.txt > rep1_vs_rep2_conserved_peaks_by_IDR.txt
+For full usage, try 'idr h'
+{{{
+idr --samples My_TF_rep_1.narrowPeak My_TF_rep_2.narrowPeak --input-file-type narrowPeak --output-file My_TF.IDR.txt --plot
 }}}