Changes between Version 24 and Version 25 of SOPs/rna-seq-diff-expressions

Timestamp:

11/13/15 14:32:56 (9 years ago)

Author:

ibarrasa

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -45 +45 @@
       * to quantify transcripts and genes in a GTF file (ex: bsub cufflinks -G gene_models.gtf accepted_hits.bam)
       * to quantify transcripts, potentially novel, annotated by cufflinks (ex: bsub cufflinks accepted_hits.bam)
-      * NOTE: Some genes, although present in a GTF annotation file, may not get quantified by cufflinks.  This occurs for genes found in very long regions of overlapping genes (which exceed the default value for --max-bundle-length).  When this occurs, the standard err output of cufflinks (contained in the long LSF email when cufflinks is run via 'bsub') will contain the message "Warning: Skipping large bundle."  To correct this (or prevent it in the first place), add an argument like '--max-bundle-length 10000000' to the cufflinks command.  You may want to compare the list of genes in the GTF file to that of the cufflinks output to verify that they match.
+      * NOTE: Some genes, although present in a GTF annotation file, may not get quantified by cufflinks.  This occurs for genes found in very long regions of overlapping genes (which exceed the default value for --max-bundle-length).  When this occurs, the standard err output of cufflinks (contained in the long LSF email when cufflinks is run via 'bsub') will contain the message "Warning: Skipping large bundle."  To correct this (or prevent it in the first place), add an argument like '--max-bundle-length 10000000' to the cufflinks command. You may want to compare the list of genes in the GTF file to that of the cufflinks output to verify that they match.
 
 {{{
@@ -51 +51 @@
             cut -f1 cufflinks_output/genes.fpkm_tracking | grep -v tracking_id > cufflinks_genes.txt
 }}}
-
+    
+        * If you only want to quantify genes in your GTF file use the -G option (instead of -g which will give also transcripts found by Cufflinks and will take away counts from transcripts in your gtf file).
+     * A second option to get fpkm is to use Cuffquant and Cuffnorm as described here  [[http://cole-trapnell-lab.github.io/monocle-release/getting-started/]] and here [[http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/|cuffnorm]]. The default normalization for Cuffnorm is the same than the normalization performed by DEseq.
   * **Gene filtering**
     * Remove from the analysis any genes with 0 counts across all samples.  Some analysis tools do this themselves.