Mercurial > repos > mingchen0919 > aurora_star_site
comparison aurora_star_site.Rmd @ 0:5f6352750d82 draft
planemo upload
author | mingchen0919 |
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date | Sun, 04 Mar 2018 11:42:48 -0500 |
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-1:000000000000 | 0:5f6352750d82 |
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1 --- | |
2 title: 'STAR: RNA-Seq aligner' | |
3 output: html_document | |
4 --- | |
5 | |
6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
7 knitr::opts_chunk$set( | |
8 echo = as.logical(opt$X_e), | |
9 error = TRUE | |
10 ) | |
11 ``` | |
12 | |
13 | |
14 ## Generating genome indexes | |
15 | |
16 ```{bash} | |
17 cd ${X_d} | |
18 # create genome directory for genome indexes | |
19 mkdir -p ${X_d}/genomeDir | |
20 | |
21 cat >temp.sh <<EOF | |
22 STAR \\ | |
23 --runMode genomeGenerate \\ | |
24 --genomeDir ${X_d}/genomeDir \\ | |
25 --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\ | |
26 --sjdbGTFfile ${X_B} \\ | |
27 --sjdbOverhang ${X_C} \\ | |
28 > /dev/null 2>&1 | |
29 EOF | |
30 | |
31 grep -v None temp.sh > index-genome.sh | |
32 | |
33 # run star | |
34 sh index-genome.sh | |
35 ``` | |
36 | |
37 | |
38 ```{r} | |
39 # display index-genome code | |
40 index_genome_sh = paste0(opt$X_d, '/index-genome.sh') | |
41 tags$code(tags$pre(readChar(index_genome_sh, file.info(index_genome_sh)$size ))) | |
42 ``` | |
43 | |
44 ## Running mapping jobs | |
45 | |
46 ```{bash} | |
47 cd ${X_d} | |
48 | |
49 cat >temp.sh <<EOF | |
50 STAR \\ | |
51 --genomeDir ${X_d}/genomeDir \\ | |
52 --readFilesIn \\ | |
53 ${X_F} \\ | |
54 ${X_R} \\ | |
55 > /dev/null 2>&1 | |
56 EOF | |
57 | |
58 grep -v None temp.sh > mapping.sh | |
59 | |
60 # run mapping | |
61 sh mapping.sh | |
62 ``` | |
63 | |
64 | |
65 ```{r} | |
66 # display mapping code | |
67 mapping_sh = paste0(opt$X_d, '/mapping.sh') | |
68 tags$code(tags$pre(readChar(mapping_sh, file.info(mapping_sh)$size ))) | |
69 ``` | |
70 | |
71 | |
72 ## SAM to sorted BAM | |
73 | |
74 ```{bash} | |
75 cd ${X_d} | |
76 | |
77 echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh | |
78 | |
79 sh sam2bam.sh | |
80 | |
81 cp Aligned.out.sorted.bam ${X_S} | |
82 ``` | |
83 | |
84 ```{r} | |
85 # display sam to bam code | |
86 sam2bam_sh = paste0(opt$X_d, '/sam2bam.sh') | |
87 tags$code(tags$pre(readChar(sam2bam_sh, file.info(sam2bam_sh)$size ))) | |
88 ``` | |
89 | |
90 ## Mapping statistics | |
91 | |
92 ```{bash} | |
93 cd ${X_d} | |
94 samtools flagstat Aligned.out.sorted.bam | |
95 ``` |