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11
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1 ---
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2 title: 'Per base N content'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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9 ---
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10
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = ECHO,
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14 error = TRUE
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15 )
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16 ```
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17
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18 ### Per base N content
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19
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20 ```{r 'Per base N content', fig.width=10}
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21 ## reads 1
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22 pbNc_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base N content')
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23 pbNc_1$id = 1:length(pbNc_1$X.Base)
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24 pbNc_1$trim = 'before'
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25
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26 ## reads 2
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27 pbNc_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base N content')
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28 pbNc_2$id = 1:length(pbNc_2$X.Base)
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29 pbNc_2$trim = 'after'
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30
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31 comb_pbNc = rbind(pbNc_1, pbNc_2)
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32 comb_pbNc$trim = factor(levels = c('before', 'after'), comb_pbNc$trim)
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33
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34 p = ggplot(data = comb_pbNc, aes(x = id, y = N.Count)) +
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35 geom_line(color = 'red') +
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36 scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) +
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37 facet_grid(. ~ trim) +
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38 ylim(0, 1) +
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39 xlab('N-Count') +
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40 ylab('') +
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41 theme(axis.text.x = element_text(angle=45))
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42 ggplotly(p)
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43 ``` |
