--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/05_per_base_sequence_content.Rmd	Tue Feb 27 10:37:12 2018 -0500
@@ -0,0 +1,43 @@
+---
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = as.logical(opt$X_e),
+  error = TRUE,
+  eval = TRUE
+)
+```
+
+
+# Per base sequence content
+
+```{r 'Per base sequence content', fig.width=10}
+## reads 1
+pbsc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per base sequence content')
+pbsc_1$id = 1:length(pbsc_1$X.Base)
+
+melt_pbsc_1 = melt(pbsc_1, id=c('X.Base', 'id'))
+melt_pbsc_1$trim = 'before'
+
+
+## reads 2
+pbsc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per base sequence content')
+pbsc_2$id = 1:length(pbsc_2$X.Base)
+
+melt_pbsc_2 = melt(pbsc_2, id=c('X.Base', 'id'))
+melt_pbsc_2$trim = 'after'
+
+comb_pbsc = rbind(melt_pbsc_1, melt_pbsc_2)
+comb_pbsc$trim = factor(levels = c('before', 'after'), comb_pbsc$trim)
+
+p = ggplot(data = comb_pbsc, aes(x = id, y = value, color = variable)) +
+  geom_line() +
+  facet_grid(. ~ trim) +
+  xlim(min(comb_pbsc$id), max(comb_pbsc$id)) + 
+  ylim(0, 100) +
+  xlab('Position in read (bp)') +
+  ylab('')
+ggplotly(p)
+```
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