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1
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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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0
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10
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1
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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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0
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18
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19 # Run FastQC
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20
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21 ```{bash eval=TRUE,echo=FALSE}
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22 cd ${X_d}
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23 cp ${X_r} ${X_d}/read_1.fq
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24 cp ${X_R} ${X_d}/read_2.fq
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25
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6
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26 mkdir -p read_1 read_2
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0
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27 cat >temp.sh <<EOL
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28 fastqc \\
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29 -q \\
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30 -c ${X_c} \\
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31 -l ${X_l} \\
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32 ${X_d}/read_1.fq > /dev/null 2>&1
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33
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34 fastqc \\
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35 -q \\
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36 -c ${X_c} \\
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37 -l ${X_l} \\
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38 ${X_d}/read_2.fq > /dev/null 2>&1
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39 EOL
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40
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41 grep -v None temp.sh > fastqc.sh
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42
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43 # run fastqc
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44 sh fastqc.sh
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45
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46 # unzip outputs
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47 unzip -q read_1_fastqc.zip
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48 unzip -q read_2_fastqc.zip
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49 ```
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50
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51 ```{r}
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52 # display fastqc job script
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53 fastqc_sh = paste0(opt$X_d, '/fastqc.sh')
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54 tags$code(tags$pre(readChar(fastqc_sh, file.info(fastqc_sh)$size )))
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55 ```
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56
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57 # Raw FastQC reports
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58
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59 ## Before trimming
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60 ```{r eval=TRUE}
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61 ori_html = tags$a(href = 'read_1_fastqc/fastqc_report.html', opt$X_n)
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62 ori_fastqc_data = tags$a(href = 'read_1_fastqc/fastqc_data.txt', 'fastqc_data.txt')
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63 ori_summary = tags$a(href = 'read_1_fastqc/summary.txt', 'summary.txt')
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64 tags$ul(
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65 tags$li(ori_html),
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66 tags$li(ori_fastqc_data),
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67 tags$li(ori_summary)
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68 )
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69 ```
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70
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71 ## After trimming
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72 ```{r eval=TRUE}
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73 ori_html = tags$a(href = 'read_2_fastqc/fastqc_report.html', opt$X_n)
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74 ori_fastqc_data = tags$a(href = 'read_2_fastqc/fastqc_data.txt', 'fastqc_data.txt')
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75 ori_summary = tags$a(href = 'read_2_fastqc/summary.txt', 'summary.txt')
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76 tags$ul(
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77 tags$li(ori_html),
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78 tags$li(ori_fastqc_data),
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79 tags$li(ori_summary)
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80 )
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81 ```
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82
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83
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84 # Fastqc Output Visualization
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85
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86 ## Overview
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87
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88 ```{r eval=TRUE}
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3
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89 read_1_summary = read.csv(paste0(opt$X_d, '/read_1_fastqc/summary.txt'),
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90 stringsAsFactors = FALSE,
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91 header = FALSE, sep = '\t')[, 2:1]
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92 read_2_summary = read.csv(paste0(opt$X_d, '/read_2_fastqc/summary.txt'),
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93 stringsAsFactors = FALSE,
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94 header = FALSE, sep = '\t')[, 1]
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95 combined_summary = data.frame(read_1_summary, read_2_summary, stringsAsFactors = FALSE)
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96 names(combined_summary) = c('MODULE', 'Pre-trimming', 'Post-trimming')
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0
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97 combined_summary[combined_summary == 'FAIL'] = 'FAIL (X)'
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98 combined_summary[combined_summary == 'WARN'] = 'WARN (!)'
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99 knitr::kable(combined_summary)
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100 ```
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3
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101
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102 ```{r 'function definition', echo=FALSE}
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103 extract_data_module = function(fastqc_data, module_name, header = TRUE, comment.char = "") {
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104 f = readLines(fastqc_data)
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105 start_line = grep(module_name, f)
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106 end_module_lines = grep('END_MODULE', f)
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107 end_line = end_module_lines[which(end_module_lines > start_line)[1]]
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108 module_data = f[(start_line+1):(end_line-1)]
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109 writeLines(module_data, '/tmp/temp.txt')
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110 read.csv('/tmp/temp.txt', sep = '\t', header = header, comment.char = comment.char)
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111 }
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112 ```
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