cont. cs analysis

dge_workflow/dge_master_template.sh

@@ -66,7 +66,7 @@ mcdir $baseDir/cuffdiff
 gtfFile=$igenome/Annotation/Genes/genes.gtf
 
 ## define labels to split bam files into replicate groups
-#labels="big_cyst,small_cyst"
+#labels=$(csvcut -t -c1 $baseDir/lanereps_pooled/sample2replicates.txt | tail -n+2 | uniq | xargs echo | sed 's/ /,/g')
 labels=<<<<TBD>>>>
 
 dge_cuffdiff $gtfFile $baseDir/mapped $labels

dge_workflow/tophat_qc.R

@@ -81,4 +81,6 @@ ggplot(algnSummary, aes(condition, mapped_reads)) +
 #' Without using any transcriptome as reference, the genome can be binned and alignment counts per bin can be used to perform a correlation analysis.
 #' Used tool [deepTools](https://github.com/fidelram/deepTools)
 
-### todo integrate bam correlation analysis
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+## http://stackoverflow.com/questions/291813/recommended-way-to-embed-pdf-in-html
+#+ results="asis"
+cat("<embed src=\"./bc.pdf\" width=\"1100px\" height=\"1000px\">")
\ No newline at end of file