Changes between Version 21 and Version 22 of SOP/PooledCRISPR

Timestamp:

12/07/21 12:39:02 (3 years ago)

Author:

thiruvil

Comment:

--

SOP/PooledCRISPR

@@ -95 +95 @@
 # use the option --normcounts-to-file to write normalized counts (by guide) to a file
 
-# A summary of the output (in pdf) is available from running the R script (see below).  In
-# some versions of 0.5.9+ an error may occur for the 'paired' option,
+# If control guides are used, these can be specified using the options (below).
+# MAGeCK will use the control guides for normalization and generating the null distribution in running RRA, instead of all the guides.
+--control-sgrna controlGuides.txt --norm-method control
+
+#One option is to run with and without control guides and compare the results, e.g. volcano plot of -log(RRA) vs logFC to see how the control guides compare.
+
+# A summary of the output (in pdf) is available from running the R script (see below).
+# In some versions of 0.5.9+ an error may occur for the 'paired' option,
 # Error in axis(1, at = 1:length(vali), labels = (collabel), las = 2) :
 #'at' and 'labels' lengths differ, 2 != 4
@@ -102 +108 @@
 # e.g.  collabel=c("low","high")
 # in the R script for all occurrences
+
 
 }}}