Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison fastqc_report.Rmd @ 0:b7c115edd970 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author mingchen0919
date Tue, 27 Feb 2018 10:37:12 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:b7c115edd970
1 ---
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
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = as.logical(opt$X_e),
14 error = TRUE,
15 eval = TRUE
16 )
17 ```
18
19
20
21
22
23 ##
24
25 ##
26
27
28 ##
29
30
31 ##
32
33 ##
34
35 ##
36
37 ### Kmer Content {.tabset}
38
39 #### Before
40
41 ```{r 'Kmer Content (before)', fig.width=10}
42 kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content')
43 knitr::kable(kc_1)
44 ```
45
46 #### After
47 ```{r 'Kmer Content (after)', fig.width=10}
48 kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content')
49 knitr::kable(kc_2)
50 ```
51
52
53 # Session Info
54
55 ```{r 'session info'}
56 sessionInfo()
57 ```
58
59 # References
60
61 * Bioinformatics, Babraham (2014). FastQC.
62
63 * Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6.
64
65 * Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29.
66
67 * Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. [Link]
68
69 * Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago