Changes between Version 39 and Version 40 of SOPs/rna-seq-diff-expressions

Timestamp:

05/17/17 10:43:27 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -65 +65 @@
 }}}
     * For some analyses (or for visualization), you can add a pseudocount (such as 1 or another small number) to all genes in all samples to prevent log2 ratios that require dividing by 0 and reduce background count noise -- BUT be aware that some statistical methods (like DESeq) require raw input values without any pseudocounts or normalization. 
+    * **NOTE:**
+      * Both htseq-count and featureCounts ignore multi-mapped reads (ie. these will not get counted) by default.  In featureCounts use -M option to count multi-mapped reads, if needed.
+      * Summary reported by both htseq-count (at the bottom of output file) and featureCounts is with respect to number of records (ie. lines) in the bam file, to summarize per read further parsing may be needed: extra information can be obtained from i) htseq-count use -o option and ii) featureCounts use -R option.
+
 
   * **Quantification by FPKM (Fragments Per Kilobase of transcript per Million mapped reads)**