Changes between Version 26 and Version 27 of SOPs/rna-seq-diff-expressions

Timestamp:

01/13/16 09:21:08 (9 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -45 +45 @@
          * ''featureCounts -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam'' (single-end reads)
          * ''featureCounts -p -a gene_anotations.gtf -o MySample.featureCounts.txt MySample.bam'' (paired-end reads)
-
-    * For custom analyses, 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. 
+    * 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. 
 
   * **Quantification of FPKM values**