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author mingchen0919
date Sun, 30 Dec 2018 13:11:48 -0500
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1 ---
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2 title: 'STAR: RNA-Seq aligner'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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7
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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10 ```
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11
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12 ```{css, echo=FALSE}
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13 pre code, pre, code {
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14 white-space: pre !important;
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15 overflow-x: scroll !important;
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16 word-break: keep-all !important;
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17 word-wrap: initial !important;
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18 }
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19 ```
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20
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21 ```{r, echo=FALSE}
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22 # to make the css theme to work, <link></link> tags cannot be added directly
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23 # as <script></script> tags as below.
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24 # it has to be added using a code chunk with the htmltool functions!!!
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25 css_link = tags$link()
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26 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
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27 css_link
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28 ```
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29
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30 ```{r, eval=FALSE, echo=FALSE}
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31 # this code chunk is purely for adding comments
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32 # below is to add jQuery and jstree javascripts
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33 ```
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34
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35 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
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36
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37
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38 ```{r, eval=FALSE, echo=FALSE}
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39 # this code chunk is purely for adding comments
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40 # javascript code below is to build the file tree interface
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41 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
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42 ```
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43 <script>
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44 jQuery(function () {
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45 // create an instance when the DOM is ready
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46 jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
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47 window.open( data.node.a_attr.href, data.node.a_attr.target )
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48 });
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49 });
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50 </script>
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51
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52
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53 ```{r, eval=FALSE, echo=FALSE}
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54 ---
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55 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
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56 ---
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57 ```
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58
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59 ## Job scripts
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60
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61 ```{bash, echo=FALSE}
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62 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
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63 ```
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64
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65 ### Index genome
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66
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67 ```{r echo=FALSE,results='asis'}
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68 # display content of the job-script.sh file.
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69 cat('```bash\n')
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70 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/index-genome.sh')), sep = '\n')
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71 cat('\n```')
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72 ```
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73
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74 ### Mapping
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75
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76 ```{r echo=FALSE,results='asis'}
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77 # display content of the job-script.sh file.
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78 cat('```bash\n')
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79 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/mapping.sh')), sep = '\n')
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80 cat('\n```')
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81 ```
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82
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83 ### SAM to sorted BAM
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84
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85 ```{r echo=FALSE,warning=FALSE,results='asis'}
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86 # display content of the job-script.sh file.
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87 cat('```bash\n')
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88 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/sam2bam.sh')), sep = '\n')
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89 cat('\n```')
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90 ```
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91
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92 ### Mapping evaluation
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93
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94 ```{r echo=FALSE,warning=FALSE,results='asis'}
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95 # display content of the job-script.sh file.
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96 cat('```bash\n')
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97 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.sh')), sep = '\n')
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98 cat('\n```')
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99 ```
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100
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101
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102 ### Mapping evaluation results
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103
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104 ```{r echo=FALSE,warning=FALSE,results='asis'}
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105 # display content of the job-script.sh file.
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106 cat('```bash\n')
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107 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n')
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108 cat('\n```')
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109 ```
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110