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0
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1
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2
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3
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4 # Run FastQC
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5
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6 ```{bash eval=TRUE,echo=FALSE}
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7 cd ${X_d}
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8 cp ${X_r} ${X_d}/read_1.fq
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9 cp ${X_R} ${X_d}/read_2.fq
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10
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11 mkdir -p read_1 read_2
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12 cat >temp.sh <<EOL
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13 fastqc \\
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14 -q \\
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15 -c ${X_c} \\
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16 -l ${X_l} \\
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17 ${X_d}/read_1.fq > /dev/null 2>&1
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18
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19 fastqc \\
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20 -q \\
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21 -c ${X_c} \\
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22 -l ${X_l} \\
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23 ${X_d}/read_2.fq > /dev/null 2>&1
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24 EOL
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25
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26 grep -v None temp.sh > fastqc.sh
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27
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28 # run fastqc
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29 sh fastqc.sh
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30
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31 # unzip outputs
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32 unzip -q read_1_fastqc.zip
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33 unzip -q read_2_fastqc.zip
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34 ```
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35
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36 ```{r}
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37 # display fastqc job script
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38 fastqc_sh = paste0(opt$X_d, '/fastqc.sh')
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39 tags$code(tags$pre(readChar(fastqc_sh, file.info(fastqc_sh)$size )))
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40 ```
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41
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42 # Raw FastQC reports
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43
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44 ## Before trimming
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45 ```{r eval=TRUE}
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46 ori_html = tags$a(href = 'read_1_fastqc/fastqc_report.html', opt$X_n)
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47 ori_fastqc_data = tags$a(href = 'read_1_fastqc/fastqc_data.txt', 'fastqc_data.txt')
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48 ori_summary = tags$a(href = 'read_1_fastqc/summary.txt', 'summary.txt')
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49 tags$ul(
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50 tags$li(ori_html),
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51 tags$li(ori_fastqc_data),
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52 tags$li(ori_summary)
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53 )
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54 ```
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55
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56 ## After trimming
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57 ```{r eval=TRUE}
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58 ori_html = tags$a(href = 'read_2_fastqc/fastqc_report.html', opt$X_n)
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59 ori_fastqc_data = tags$a(href = 'read_2_fastqc/fastqc_data.txt', 'fastqc_data.txt')
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60 ori_summary = tags$a(href = 'read_2_fastqc/summary.txt', 'summary.txt')
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61 tags$ul(
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62 tags$li(ori_html),
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63 tags$li(ori_fastqc_data),
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64 tags$li(ori_summary)
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65 )
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66 ```
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67
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68
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69 # Fastqc Output Visualization
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70
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71 ## Overview
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72
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73 ```{r eval=TRUE}
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74 read_1_summary = read.csv(paste0(opt$X_d, '/read_1_fastqc/summary.txt'), header = FALSE, sep = '\t')[, 2:1]
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75 read_2_summary = read.csv(paste0(opt$X_d, '/read_2_fastqc/summary.txt'), header = FALSE, sep = '\t')[, 1]
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76 combined_summary = cbind(read_1_summary, read_2_summary)
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77 names(combined_summary) = c('MODULE', paste0(opt$X_n, '(before)'), paste0(opt$X_N, '(after)'))
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78 combined_summary[combined_summary == 'FAIL'] = 'FAIL (X)'
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79 combined_summary[combined_summary == 'WARN'] = 'WARN (!)'
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80 knitr::kable(combined_summary)
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81 ```
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