Changes between Version 17 and Version 18 of SOPs/InProgress

Timestamp:

05/13/14 18:31:38 (11 years ago)

Author:

byuan

Comment:

--

SOPs/InProgress

@@ -4 +4 @@
 === Use macs2 to get peaks (not macs14): You can adjust fragment length with --nomodel --shiftsize if NSC/RSC plots are not good ===
 {{{
+# -B create bedgraph
+# -p 1e -3 : p values as 1e -3
 bsub macs2 callpeak -t IP_1.bam -c control_1.bam  -f BAM -g hs -n IP.1_vs_control.1 -B  -p 1e-3
 bsub macs2 callpeak -t IP_2.bam -c control_2.bam  -f BAM -g hs -n IP.2_vs_control.2 -B  -p 1e-3
@@ -17 +19 @@
 {{{
 # chromInfo.txt format: chromosome<tab>size
+# -1 (one) not l, 0 F p.value are fixed. Use p.value as the ranking measure.
+# rep1_vs_rep2_IDR is used for output file names
 Rscript 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 
 }}}
@@ -22 +26 @@
 === Plot the IDR plots: ===
 {{{
+ # This R script can also take multiple comparisons, please refer to https://sites.google.com/site/anshulkundaje/projects/idr for detail.
  Rscript batch-consistency-plot.r 1 rep1_vs_rep2_IDR_plot rep1_vs_rep2_IDR
 }}}