Changes between Version 50 and Version 51 of SOPs/rna-seq-diff-expressions

Timestamp:

06/20/17 14:07:18 (8 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -101 +101 @@
     * Method 3: Use Cuffquant to get '''normalized''' FPKMs, as described with [http://cole-trapnell-lab.github.io/monocle-release/getting-started/ monocle] and [http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/#running-cuffnorm Cuffnorm]. The default normalization for Cuffnorm is the same as the normalization performed by DESeq.
 
-    * Method 4: Use featureCounts
-      * Gene-level FPKM values are calculated from gene-level counts, corrected for library size and "gene length", as defined by the length of the non-redundant overlap of all exons of all transcripts of that gene.  Typically this method overestimates gene length since the length of a gene is by definition at least as long as every transcript defining the gene.
+    * Method 4: Use featureCounts to get gene lengths
+      * With gene-level counts and gene lengths, one can use a spreadsheet or statistics program to calculate FPKM.
+      * "Gene length" is defined by the length of the non-redundant overlap of all exons of all transcripts of that gene.  Typically this method overestimates gene length since the length of a gene is by definition at least as long as every transcript defining the gene.
 
   * **Gene filtering**