Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison 11_kmer_content.Rmd @ 2:c64267b9f754 draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
parents b7c115edd970
children
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1:92e3de11b9f8 2:c64267b9f754
1 --- 1 ---
2 output: html_document 2 output: html_document
3 --- 3 ---
4 4
5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} 5 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
6 knitr::opts_chunk$set( 6 knitr::opts_knit$set(progress = FALSE)
7 echo = as.logical(opt$X_e), 7 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
8 error = TRUE,
9 eval = TRUE
10 )
11 ``` 8 ```
12 9
13 # Kmer Content {.tabset} 10 ### Kmer Content {.tabset}
14 11
15 ## Before 12 #### Before
16 13
17 ```{r 'Kmer Content (before)', fig.width=10} 14 ```{r 'Kmer Content (before)', fig.width=10}
18 kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content') 15 kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content')
19 knitr::kable(kc_1) 16 knitr::kable(kc_1)
20 ``` 17 ```
21 18
22 ## After 19 #### After
23 ```{r 'Kmer Content (after)', fig.width=10} 20 ```{r 'Kmer Content (after)', fig.width=10}
24 kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content') 21 kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content')
25 knitr::kable(kc_2) 22 knitr::kable(kc_2)
26 ``` 23 ```
24