changeset 1:92e3de11b9f8 draft

remove fastqc_report.Rmd

--- a/fastqc_report.Rmd	Tue Feb 27 10:37:12 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
----
-title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = as.logical(opt$X_e),
-  error = TRUE,
-  eval = TRUE
-)
-```
-
-
-
-
-
-##
-
-##
-
-
-##
-
-
-##
-
-##
-
-##
-
-### Kmer Content {.tabset}
-
-#### Before
-
-```{r 'Kmer Content (before)', fig.width=10}
-kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content')
-knitr::kable(kc_1)
-```
-
-#### After
-```{r 'Kmer Content (after)', fig.width=10}
-kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content')
-knitr::kable(kc_2)
-```
-
-
-# Session Info
-
-```{r 'session info'}
-sessionInfo()
-```
-
-# References
-
-* Bioinformatics, Babraham (2014). FastQC.
-
-* Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6.
-
-* Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29.
-
-* Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. [Link]
-
-* Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago