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2
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1 ---
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15
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2 title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
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14
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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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2
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9 ---
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10
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14
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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 = ECHO
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14 )
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2
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15 ```
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16
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17
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14
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18 # Fastqc Analysis
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2
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19
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14
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20 * Copy fastq files to job working directory
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21
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22 ```{bash 'copy files'}
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2
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23 for f in $(echo READS | sed "s/,/ /g")
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24 do
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25 cp $f ./
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26 done
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27 ```
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28
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14
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29 * Run fastqc
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2
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30
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31 ```{bash 'run fastqc'}
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2
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32 for r in $(ls *.dat)
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33 do
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34 fastqc -o REPORT_DIR $r > /dev/null 2>&1
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2
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35 done
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36 ```
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37
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15
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38 ## Evaluation results
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2
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39
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40 ```{r 'html report links'}
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41 html_file = list.files('REPORT_DIR', pattern = '.*html')
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42 tags$ul(tags$a(href=html_file, paste0('HTML report', opt$name)))
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43 ```
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44
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45
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46 ```{r 'extract fastqc_data.txt and summary.txt'}
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47 # list all zip files
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48 zip_file = list.files(path = 'REPORT_DIR', pattern = '.zip')
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49 unzip(paste0('REPORT_DIR/', zip_file), exdir = 'REPORT_DIR')
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50
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51 unzip_directory = paste0(tail(strsplit(opt$reads, '/')[[1]], 1), '_fastqc/')
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52 fastqc_data_txt_path = paste0('REPORT_DIR/', unzip_directory, 'fastqc_data.txt')
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53 summary_txt_path = paste0('REPORT_DIR/', unzip_directory, 'summary.txt')
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2
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54 ```
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55
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15
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56
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57 ```{r 'summary.txt'}
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58 tags$ul(tags$a(href=paste0(unzip_directory, 'summary.txt'), 'summary.txt'))
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59 ```
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60
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61
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62 ```{r 'fastqc_data.txt'}
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63 tags$ul(tags$a(href=paste0(unzip_directory, 'fastqc_data.txt'), 'fastqc_data.txt'))
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64 ```
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65
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66
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67 # Fastqc output visualization
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68
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69 ## Overview
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70
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71 ```{r}
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72 # read.table(fastqc_data_txt_path)
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73 summary_txt = read.csv(summary_txt_path, header = FALSE, sep = '\t')[, 2:1]
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74 names(summary_txt) = c('MODULE', 'PASS/FAIL')
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75 knitr::kable(summary_txt)
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76 ```
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77
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78 ## Summary by module {.tabset}
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2
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79
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14
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80 * Define a function to extract outputs for each module from fastqc output
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2
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81
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14
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82 ```{r 'function definition'}
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83 extract_data_module = function(fastqc_data, module_name) {
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84 f = readLines(fastqc_data)
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85 start_line = grep(module_name, f)
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86 end_module_lines = grep('END_MODULE', f)
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87 end_line = end_module_lines[which(end_module_lines > start_line)[1]]
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88 module_data = f[(start_line+1):(end_line-1)]
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89 writeLines(module_data, 'temp.txt')
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90 read.csv('temp.txt', sep = '\t')
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2
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91 }
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92 ```
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93
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15
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94 ### Per base sequence quality
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95
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96 ```{r}
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97 pbsq = extract_data_module(fastqc_data_txt_path, 'Per base sequence quality')
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98 knitr::kable(pbsq)
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99 ```
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100
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101 ### Per tile sequence quality
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102
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103 ```{r}
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104 ptsq = extract_data_module(fastqc_data_txt_path, 'Per tile sequence quality')
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105 knitr::kable(ptsq)
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106 ```
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107
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108
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2
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109
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14
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110 # Session Info
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2
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111
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14
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112 ```{r 'session info'}
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113 sessionInfo()
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2
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114 ```
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115
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