Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site
annotate 01_evaluation_overview.Rmd @ 12:68ea2ebbf866 draft
add boxplot for per base sequence quality
| author | mingchen0919 |
|---|---|
| date | Thu, 09 Nov 2017 09:23:43 -0500 |
| parents | 507eec497730 |
| children |
| rev | line source |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
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1 --- |
| 11 | 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 | |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
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9 --- |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
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10 |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} |
| 11 | 12 knitr::opts_chunk$set( |
| 13 echo = ECHO, | |
| 14 error = TRUE | |
| 15 ) | |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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16 ``` |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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17 |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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18 |
| 11 | 19 # Fastqc Evaluation |
| 20 | |
| 21 ## Evaluation of reads before trimming | |
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0
d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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22 |
| 11 | 23 ```{r} |
| 24 if ('READS_1' == 'None') { | |
| 25 stop("No pre-trimming reads provided!") | |
| 26 } else { | |
| 27 ## run fastqc evaluation | |
| 28 fastqc_command = paste0('fastqc ') %>% | |
| 29 (function(x) { | |
| 30 ifelse('CONTAMINANTS' != 'None', paste0(x, '-c CONTAMINANTS '), x) | |
| 31 }) %>% | |
| 32 (function(x) { | |
| 33 ifelse('LIMITS' != 'None', paste0(x, '-l LIMITS '), x) | |
| 34 }) %>% | |
| 35 (function(x) { | |
| 36 paste0(x, '-o REPORT_DIR ') | |
| 37 }) | |
| 38 fastqc_command_reads_1 = paste0(fastqc_command, 'READS_1 > /dev/null 2>&1') | |
| 39 system(fastqc_command_reads_1, intern = TRUE) | |
| 40 | |
| 41 # Original html report | |
| 42 reads_1_base = tail(strsplit('READS_1', '/')[[1]], 1) | |
| 43 original_html = tags$a(href=paste0(reads_1_base, '_fastqc.html'), paste0('HTML report: ', opt$name_1)) | |
| 44 | |
| 45 unzip(paste0('REPORT_DIR/', reads_1_base, '_fastqc.zip'), exdir = 'REPORT_DIR') | |
| 46 reads_1_unzip = paste0('REPORT_DIR/', reads_1_base, '_fastqc/') | |
| 47 # fastqc_data.txt | |
| 48 file.copy(paste0(reads_1_unzip, 'fastqc_data.txt'), 'REPORT_DIR/reads_1_fastqc_data.txt') | |
| 49 fastqc_data = tags$a(href='reads_1_fastqc_data.txt', paste0('fastqc_data.txt: ', opt$name_1)) | |
| 50 # summary.txt | |
| 51 file.copy(paste0(reads_1_unzip, 'summary.txt'), 'REPORT_DIR/reads_1_summary.txt') | |
| 52 summary_data = tags$a(href='reads_1_summary.txt', paste0('summary.txt: ', opt$name_1)) | |
| 53 | |
| 54 tags$ul( | |
| 55 tags$li(original_html), | |
| 56 tags$li(fastqc_data), | |
| 57 tags$li(summary_data) | |
| 58 ) | |
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0
d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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59 } |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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60 ``` |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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61 |
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d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
|
62 |
| 11 | 63 ## Evaluation of reads after trimming |
| 64 | |
|
0
d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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65 ```{r} |
| 11 | 66 if ('READS_2' == 'None') { |
| 67 stop("No pre-trimming reads provided!") | |
| 68 } else { | |
| 69 ## run fastqc evaluation | |
| 70 fastqc_command = paste0('fastqc ') %>% | |
| 71 (function(x) { | |
| 72 ifelse('CONTAMINANTS' != 'None', paste0(x, '-c CONTAMINANTS '), x) | |
| 73 }) %>% | |
| 74 (function(x) { | |
| 75 ifelse('LIMITS' != 'None', paste0(x, '-l LIMITS '), x) | |
| 76 }) %>% | |
| 77 (function(x) { | |
| 78 paste0(x, '-o REPORT_DIR ') | |
| 79 }) | |
| 80 fastqc_command_reads_2 = paste0(fastqc_command, 'READS_2 > /dev/null 2>&1') | |
| 81 system(fastqc_command_reads_2, intern = TRUE) | |
| 82 | |
| 83 # Original html report | |
| 84 reads_2_base = tail(strsplit('READS_2', '/')[[1]], 1) | |
| 85 original_html = tags$a(href=paste0(reads_2_base, '_fastqc.html'), paste0('HTML report: ', opt$name_2)) | |
| 86 | |
| 87 unzip(paste0('REPORT_DIR/', reads_2_base, '_fastqc.zip'), exdir = 'REPORT_DIR') | |
| 88 reads_2_unzip = paste0('REPORT_DIR/', reads_2_base, '_fastqc/') | |
| 89 # fastqc_data.txt | |
| 90 file.copy(paste0(reads_2_unzip, 'fastqc_data.txt'), 'REPORT_DIR/reads_2_fastqc_data.txt') | |
| 91 fastqc_data = tags$a(href='reads_2_fastqc_data.txt', paste0('fastqc_data.txt: ', opt$name_2)) | |
| 92 # summary.txt | |
| 93 file.copy(paste0(reads_2_unzip, 'summary.txt'), 'REPORT_DIR/reads_2_summary.txt') | |
| 94 summary_data = tags$a(href='reads_2_summary.txt', paste0('summary.txt: ', opt$name_2)) | |
| 95 | |
| 96 tags$ul( | |
| 97 tags$li(original_html), | |
| 98 tags$li(fastqc_data), | |
| 99 tags$li(summary_data) | |
| 100 ) | |
|
0
d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
|
101 } |
| 11 | 102 ``` |
|
0
d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
|
103 |
| 11 | 104 |
| 105 | |
| 106 # Fastqc output visualization | |
| 107 | |
| 108 ## Overview | |
| 109 | |
| 110 ```{r} | |
| 111 reads_1_summary = read.csv('REPORT_DIR/reads_1_summary.txt', header = FALSE, sep = '\t')[, 2:1] | |
| 112 reads_2_summary = read.csv('REPORT_DIR/reads_2_summary.txt', header = FALSE, sep = '\t')[, 1] | |
| 113 combined_summary = cbind(reads_1_summary, reads_2_summary) | |
| 114 names(combined_summary) = c('MODULE', paste0(opt$name_1, '(before)'), paste0(opt$name_2, '(after)')) | |
| 115 combined_summary[combined_summary == 'FAIL'] = 'FAIL (X)' | |
| 116 combined_summary[combined_summary == 'WARN'] = 'WARN (!)' | |
| 117 knitr::kable(combined_summary) | |
| 118 ``` | |
| 119 | |
| 120 # Session Info | |
| 121 | |
| 122 ```{r 'session info'} | |
| 123 sessionInfo() | |
|
0
d732d4526c6d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
mingchen0919
parents:
diff
changeset
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124 ``` |