Changes between Version 3 and Version 4 of SOPs/geneFeatureHeatmaps

Timestamp:

05/14/14 10:52:45 (11 years ago)

Author:

gbell

Comment:

--

SOPs/geneFeatureHeatmaps

@@ -1 +1 @@
 == Creating genome feature heatmaps from sequencing experiments ==
 
+'''These types of figures are best created using the [[https://code.google.com/p/ngsplot/|ngsplot]] software package.'''
+
+Before that code was released, we used the method describe below:
 
 This type of figure can be used to visualize chIP or expression expression data in selected genome regions (rows) that have been divided into windows (columns) using either similar or relative feature widths.
@@ -17 +20 @@
   1. Quantify reads that map to each window of each region.
      * Method 1: Use coverageBed (ex: coverageBed -split -abam accepted_hits.bam -b region.windows.bed > out)
-     * Method 2: Use cufflinks (after converting region.windows.bed into a GTF file)
-     * Other methods?
+     * Method 2: Use htseq-count (after converting region.windows.bed into a GTF file)
+     * Method 3: Use cufflinks (after converting region.windows.bed into a GTF file)
    1. Convert list into matrix (with code such as /nfs/BaRC_Public/BaRC_code/Perl/convert_coverageBed_output_to_matrix.pl) like
 
@@ -30 +33 @@
   1. Add another column at the beginning with the same region IDs and save the tab-delimited text file with a cdt extension.
   2. Open the cdt matrix file in Java TreeView, adjust the pixel settings and print the figure.
-
-
-
-**Any other approaches to do this?**