In yangjl/maizeR: Generate pipelines for maize Genomic and Genetic analysis

Whole Genome Biosulfite Sequencing Mapping using Bismark

Bismark Documentation

#bowtie2/2.2.5

#http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf
#Bismark

#(I) Running bismark_genome_preparation

module load bismark/0.14.3
module load bowtie2/2.2.5
bismark_genome_preparation /home/jolyang/dbcenter/AGP/AGPv2/

#(II) Running bismark 

bismark --bowtie2 -n 1 -l 50 /data/genomes/homo_sapiens/GRCh37/ test_dataset.fastq


#(III) Running the Bismark bismark_methylation_extractor
bismark_methylation_extractor -s --comprehensive test_dataset.fastq_bismark.sam

SNP and INDEL calling using GATK

1. quartz for de novo quality score compression of fastq files.

prepare golden SNP and InDels from HapMap2 SNPs

system("cd ~/dbcenter/HapMap/HapMap2")
system("")

SNP, INDEL and SV calling using fermikit

fermikit is a de novo assembly based variant calling pipeline for Illumina short reads

Commonly use one liner

1. How To Merge Two Fastq.Gz Files? cat file1.gz file2.gz file3.gz > allfiles.gz

Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The html_vignette output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The html_vignette format:

• Never uses retina figures
• Has a smaller default figure size
• Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style

Vignette Info

Note the various macros within the vignette section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Styles

The html_vignette template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:

output: 
  rmarkdown::html_vignette:
    css: mystyles.css

Figures

The figure sizes have been customised so that you can easily put two images side-by-side.

plot(1:10)
plot(10:1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

More Examples

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

knitr::kable(head(mtcars, 10))

Also a quote using >:

"He who gives up [code] safety for [code] speed deserves neither." (via)

yangjl/maizeR documentation built on May 4, 2019, 2:28 p.m.