Changes between Version 4 and Version 5 of SOPs/rna-seq-diff-expressions

Timestamp:

03/25/13 15:27:30 (12 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -41 +41 @@
          * ''bsub  "samtools view accepted_hitsSortedByname.bam | htseq-count -m intersection-strict --stranded=no - gene_models.gtf >| gene_model.counts.txt"''
     * Remove the rows at the bottom with descriptions like no_feature, ambiguous, etc.
-    * For custom analyses, you can add a pseudocount (such as 1) 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 custom analyses, you can add a pseudocount (such as 1) 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**