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1 ---
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2 title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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9 ---
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10
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = as.logical(opt$X_e),
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14 error = TRUE,
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15 eval = TRUE
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16 )
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17 ```
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18
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19
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20
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21
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22
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23 ##
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24
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25 ##
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26
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27
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28 ##
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29
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30
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31 ##
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32
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33 ##
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34
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35 ##
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36
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37 ### Kmer Content {.tabset}
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38
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39 #### Before
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40
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41 ```{r 'Kmer Content (before)', fig.width=10}
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42 kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content')
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43 knitr::kable(kc_1)
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44 ```
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45
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46 #### After
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47 ```{r 'Kmer Content (after)', fig.width=10}
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48 kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content')
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49 knitr::kable(kc_2)
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50 ```
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51
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52
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53 # Session Info
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54
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55 ```{r 'session info'}
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56 sessionInfo()
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57 ```
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58
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59 # References
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60
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61 * Bioinformatics, Babraham (2014). FastQC.
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62
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63 * 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.
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64
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65 * Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29.
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66
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67 * 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]
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68
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69 * Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago
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