Description Usage Arguments Details Value Examples
Run bowtie2/2.2.5 Run bismark/0.14.3
1 2 3 | 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, "bigmemh", 1))
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inputdf |
An input data.frame object. Must contains fq1, fq2 and outbase, bam (optional). |
genome |
The folder of genome prepared by bismark. If genome is NULL, then genome will read from inputdf column: 'genome'. |
outdir |
Folder for output. |
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). |
align |
Whether to conduct alignment, default=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/0.14.3 module load bowtie2/2.2.5 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.
1 2 3 4 | 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)
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