run_bismark: 'Run array Bismark job on farm'
In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description Usage Arguments Details Value Examples

required modules to load: bowtie2/2.2.5 bismark/0.14.3

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run_bismark(inputdf, genome = "/home/jolyang/dbcenter/AGP/AGPv2",
  outdir = "/group/jrigrp4/BS_teo20/WGBS/BSM", N = 1, align = TRUE,
  email = NULL, runinfo = c(FALSE, "batch", 1, "10G", "8:00:00"))

`inputdf`	An input data.frame object. Must contains fq1, fq2 and outbase, bam (optional). [df, ["fq1", "fq2", "outbase", ("bam", "genome")]]
`genome`	The folder of genome prepared by bismark. If genome is NULL, then genome will read from inputdf column: 'genome'. [chr, ="/home/jolyang/dbcenter/AGP/AGPv2"]
`outdir`	Folder for output. [chr, ="/group/jrigrp4/BS_teo20/WGBS/BSM"]
`N`	Number of mismatches. Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for Bowtie 1 see -n). [num, =1]
`align`	Whether to conduct alignment, default=TRUE. [logical, =TRUE]
`email`	Your email address that farm will email to once the job was done/failed.

Allow one mismatch 'n 1'

see more detail about Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf

(I) Running bismark_genome_preparation module load bismark/0.19 module load bowtie2/2.2 module load samtools bismark_genome_preparation –bowtie2 /home/jolyang/dbcenter/AGP/AGPv2/

(II) Running bismark

#uses 0-based genomic start and 1-based end coordinates. bismark_methylation_extractor -s –bedGraph –counts –buffer_size 10G –CX –cytosine_report –genome_folder /home/jolyang/dbcenter/AGP/AGPv2 test_pe.bam #<chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

return a batch of shell scripts.

input_df <- data.frame(fq1=c("f_1.fq", "t_1.fq"), fq2=c("f_1.fq", "t_2.fq"), out=c("t1", "t2"))
runa_bismark(input_df, genome="/home/jolyang/dbcenter/AGP/AGPv2",
cpu=4, outdir="/group/jrigrp4/BS_teo20/WGBS/BSM", arrayjobs="1-5", jobid="bs1-5",
email=NULL)