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comparison 01_evaluation_overview.Rmd @ 0:b7c115edd970 draft

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planemo upload
author mingchen0919
date Tue, 27 Feb 2018 10:37:12 -0500
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children c64267b9f754
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1 ---
2 title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
3 output:
4 html_document:
5 number_sections: true
6 toc: true
7 theme: cosmo
8 highlight: tango
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = as.logical(opt$X_e),
14 error = TRUE,
15 eval = TRUE
16 )
17 ```
18
19 # Run FastQC
20
21 ```{bash eval=TRUE,echo=FALSE}
22 cd ${X_d}
23 cp ${X_r} ${X_d}/read_1.fq
24 cp ${X_R} ${X_d}/read_2.fq
25
26 cat >temp.sh <<EOL
27 fastqc \\
28 -q \\
29 -c ${X_c} \\
30 -l ${X_l} \\
31 ${X_d}/read_1.fq > /dev/null 2>&1
32
33 fastqc \\
34 -q \\
35 -c ${X_c} \\
36 -l ${X_l} \\
37 ${X_d}/read_2.fq > /dev/null 2>&1
38 EOL
39
40 grep -v None temp.sh > fastqc.sh
41
42 # run fastqc
43 sh fastqc.sh
44
45 # unzip outputs
46 unzip -q read_1_fastqc.zip
47 unzip -q read_2_fastqc.zip
48 ```
49
50 ```{r}
51 # display fastqc job script
52 fastqc_sh = paste0(opt$X_d, '/fastqc.sh')
53 tags$code(tags$pre(readChar(fastqc_sh, file.info(fastqc_sh)$size )))
54 ```
55
56 # Raw FastQC reports
57
58 ## Before trimming
59 ```{r eval=TRUE}
60 ori_html = tags$a(href = 'read_1_fastqc/fastqc_report.html', opt$X_n)
61 ori_fastqc_data = tags$a(href = 'read_1_fastqc/fastqc_data.txt', 'fastqc_data.txt')
62 ori_summary = tags$a(href = 'read_1_fastqc/summary.txt', 'summary.txt')
63 tags$ul(
64 tags$li(ori_html),
65 tags$li(ori_fastqc_data),
66 tags$li(ori_summary)
67 )
68 ```
69
70 ## After trimming
71 ```{r eval=TRUE}
72 ori_html = tags$a(href = 'read_2_fastqc/fastqc_report.html', opt$X_n)
73 ori_fastqc_data = tags$a(href = 'read_2_fastqc/fastqc_data.txt', 'fastqc_data.txt')
74 ori_summary = tags$a(href = 'read_2_fastqc/summary.txt', 'summary.txt')
75 tags$ul(
76 tags$li(ori_html),
77 tags$li(ori_fastqc_data),
78 tags$li(ori_summary)
79 )
80 ```
81
82
83 # Fastqc Output Visualization
84
85 ## Overview
86
87 ```{r eval=TRUE}
88 read_1_summary = read.csv(paste0(opt$X_d, '/read_1_fastqc/summary.txt'), header = FALSE, sep = '\t')[, 2:1]
89 read_2_summary = read.csv(paste0(opt$X_d, '/read_2_fastqc/summary.txt'), header = FALSE, sep = '\t')[, 1]
90 combined_summary = cbind(read_1_summary, read_2_summary)
91 names(combined_summary) = c('MODULE', paste0(opt$X_n, '(before)'), paste0(opt$X_N, '(after)'))
92 combined_summary[combined_summary == 'FAIL'] = 'FAIL (X)'
93 combined_summary[combined_summary == 'WARN'] = 'WARN (!)'
94 knitr::kable(combined_summary)
95 ```