Changes between Version 48 and Version 49 of SOPs/rna-seq-diff-expressions

Timestamp:

06/20/17 12:16:35 (8 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -80 +80 @@
 
     * Method 1: Use [http://cole-trapnell-lab.github.io/cufflinks/manual/ cufflinks] 
-      * This is the traditional method.
-
-      * To quantify transcripts and genes in a GTF file, use a command like 
+        * This is the traditional method.
+        * To quantify transcripts and genes in a GTF file, use a command like 
 {{{
 bsub cufflinks -G gene_models.gtf accepted_hits.bam
 }}}
-
-      * To quantify transcripts, potentially novel, annotated by cufflinks, use a command like 
+        * To quantify transcripts, potentially novel, annotated by cufflinks, use a command like 
 {{{
 bsub cufflinks accepted_hits.bam
 }}}
-
-      * Gene-level FPKM values are calculated by taking the sum of all transcript FPKMs for a gene.  As a result, no "gene length" needs to be calculated.
-      * 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.
-      * 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).
+        * Gene-level FPKM values are calculated by taking the sum of all transcript FPKMs for a gene.  As a result, no "gene length" needs to be calculated.
+        * 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.
+        * 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).
 {{{
             awk -F"\t" '{print $9}' genes.gtf | awk '{print $2}' | perl -pe 's/\"//g;s/;//g' | sort -u > gtf_genes.txt