Changes between Version 4 and Version 5 of SOPs/InProgressChipSeq

Timestamp:

05/14/14 13:08:54 (11 years ago)

Author:

ibarrasa

Comment:

--

SOPs/InProgressChipSeq

@@ -13 +13 @@
 
  * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
-=== Step 2: Calculate strand cross correlation ===
+=== Step 2: Strand cross correlation analysis ===
+ * The goal of this step is asses the quality of the IP and an estimate of the fragment size of the DNA immunoprecipitated.
  * For a detailed explanation on strand cross-correlation analysis see box 2 of this paper ([[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326|Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data ]]).
 {{{
-Rscript /nfs/BaRC_Public/phantompeakqualtools/run_spp.R -c=TreatmentIP.bam -savp -out=TreatmentIP.run_spp.out
-}}}
-
-  * After this analysis a good ChIP-seq experiment will have a second peak (reflecting the fragment size) as tall or taller than the first peak (reflecting read length). If the second peak is smaller that the first one macs will not estimate fragment size correctly. In that case we recommend running macs with parameters "--nomodel" and "--shiftsize=half_of_the_fragment_size". The fragment size is detected on the strand cross correlation analysis.
+/nfs/BaRC_Public/phantompeakqualtools/run_spp.R -c=TreatmentIP.bam -savp -out=TreatmentIP.run_spp.out
+}}}
+
+  * After this analysis a good ChIP-seq experiment will have a second peak (reflecting the fragment size) as tall or taller than the first peak (reflecting read length). Example of a good IP. If the second peak is smaller that the first (example of a weak IP) one macs will not estimate fragment size correctly. In that case we recommend running macs with parameters "--nomodel" and "--shiftsize=half_of_the_fragment_size". The fragment size is detected on the strand cross correlation analysis.
  
 === Step 3: Call peaks (bound regions) ===