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1 ---
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2 title: 'STAR: RNA-Seq aligner'
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3 output: html_document
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4 ---
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5
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6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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7 knitr::opts_chunk$set(
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8 echo = as.logical(opt$X_e),
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9 error = TRUE
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10 )
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11 ```
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12
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13
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14 ## Generating genome indexes
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15
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16 ```{bash}
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17 cd ${X_d}
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18 # create genome directory for genome indexes
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19 mkdir -p ${X_d}/genomeDir
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20
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21 cat >temp.sh <<EOF
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22 STAR \\
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23 --runMode genomeGenerate \\
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24 --genomeDir ${X_d}/genomeDir \\
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25 --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
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26 --sjdbGTFfile ${X_B} \\
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27 --sjdbOverhang ${X_C} \\
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28 > /dev/null 2>&1
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29 EOF
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30
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31 grep -v None temp.sh > index-genome.sh
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32
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33 # run star
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34 sh index-genome.sh
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35 ```
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36
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37
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38 ```{r}
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39 # display index-genome code
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40 index_genome_sh = paste0(opt$X_d, '/index-genome.sh')
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41 tags$code(tags$pre(readChar(index_genome_sh, file.info(index_genome_sh)$size )))
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42 ```
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43
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44 ## Running mapping jobs
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45
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46 ```{bash}
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47 cd ${X_d}
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48
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49 cat >temp.sh <<EOF
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50 STAR \\
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51 --genomeDir ${X_d}/genomeDir \\
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52 --readFilesIn \\
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53 ${X_F} \\
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54 ${X_R} \\
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55 > /dev/null 2>&1
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56 EOF
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57
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58 grep -v None temp.sh > mapping.sh
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59
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60 # run mapping
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61 sh mapping.sh
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62 ```
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63
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64
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65 ```{r}
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66 # display mapping code
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67 mapping_sh = paste0(opt$X_d, '/mapping.sh')
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68 tags$code(tags$pre(readChar(mapping_sh, file.info(mapping_sh)$size )))
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69 ```
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70
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71
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72 ## SAM to sorted BAM
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73
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74 ```{bash}
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75 cd ${X_d}
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76
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77 echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
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78
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79 sh sam2bam.sh
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80
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81 cp Aligned.out.sorted.bam ${X_S}
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82 ```
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83
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84 ```{r}
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85 # display sam to bam code
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86 sam2bam_sh = paste0(opt$X_d, '/sam2bam.sh')
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87 tags$code(tags$pre(readChar(sam2bam_sh, file.info(sam2bam_sh)$size )))
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88 ```
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89
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90 ## Mapping statistics
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91
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92 ```{bash}
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93 cd ${X_d}
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94 samtools flagstat Aligned.out.sorted.bam
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95 ```
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