@lakshman fixed failing star report. Now it wont mattter if bc is not yet done.

dge_workflow/star_align.sh

@@ -143,7 +143,7 @@ dge_bam_correlate . &
 #mysub "${project}__feature_counts" "featureCounts -t exon -g gene_id -a ${gtfFile} -o gene_counts.txt $(ls *bam) -T 5" -q medium | blockScript
 
 ## create tophat mapping report
-rend.R ${NGS_TOOLS}/dge_workflow/star_qc.R .
+rend.R -e ${NGS_TOOLS}/dge_workflow/star_qc.R .
 
 
 ## Condense counts into matrix

dge_workflow/star_qc.R

@@ -22,9 +22,9 @@ if(is.na(file.info(base_directory)$isdir)){
     stop(paste("base directory", base_directory, "does not exist"))
 }
 
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/ggplot_commons.R")
-require.auto(knitr)
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/ggplot_commons.R")
+require_auto(knitr)
 
 ########################################################################################################################
 #' # STAR Mapping Summary
@@ -56,6 +56,8 @@ algnSummaryLong <- ldply(list.files(base_directory, "final.out", full.names=TRUE
 algnSummary <- algnSummaryLong %>% dcast(sample ~ variable)
 algnSummary %<>% mutate(mapping_efficiency=Perc_of_reads_mapped_to_multiple_loci + Uniquely_mapped_reads_Perc)
 
+#require_auto(DT)
+#datatable(algnSummary)
 
 
 write.delim(algnSummary, file="star_mapping_stats.txt")
@@ -122,6 +124,16 @@ algnSummaryLong %>% filter(str_detect(variable, "Uniquely_mapped_reads_Perc|Perc
 #' Without using any transcriptome as reference, the genome can be binned and alignment counts per bin can be used to perform a correlation analysis.
 #' Created using [deepTools](https://github.com/fidelram/deepTools)
 
-## 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
+#' **[Open Correlation Matrix](bc.pdf)**
+
+###' <a href="bc.pdf"/>
+##+ results="asis", echo=FALSE
+##cat('<script type="text/javascript">
+##$( document ).ready(function() {
+##    console.log( "ready!" );
+##    $( "#alignment-correlation > p" ).append("<embed src=\\"./bc.pdf\\' width=\\"1100px\\' height=\\'1000px\\'>");
+##    $( "#alignment-correlation > p" ).append("<a href=\\"bc.pdf\\">Open Correlation Matrix</a>");
+##});
+##</script>
+## '
+### http://stackoverflow.com/questions/291813/recommended-way-to-embed-pdf-in-html