run_fastq_qc: 'Run fastq QC.'

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

Description

Run this 'seqtk fqchk -q 20' for all your fastq files.

Usage

run_fastq_qc(df, method = "seqtk", q = 20, email = NULL,
  runinfo = c(FALSE, "bigmemh", 1))

Arguments

df	Data.frame with fq and out columns. fq is the path of your fastq files and out is the path of your output file.
method	Method for QC, "seqtk" or "FastQC" only.
q	Default=20. Note:use -q0 to get the distribution of all quality values
email	Your email address that farm will email to once the job was done/failed.
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE 2) -p partition name, default=bigmemh and 3) –cpus, default=1. It will pass to set_array_job.
genomesize	Maize genome size, default=2500000000.

Details

dependency: seqtk version 1.0-r82-dirty

Value

return A batch of shell scripts.

Examples

fqs <- c("$HOME/dbcenter/Ecoli/fastq/SRR2921970.sra_1.fastq.gz",
         "$HOME/dbcenter/Ecoli/fastq/SRR2921970.sra_2.fastq.gz")
df <- data.frame(fq=fqs, out=fqs)
df$out <- gsub("sra_.*", "qc", df$out)
run_fastq_qc(df, email=NULL, runinfo = c(FALSE, "bigmemh", 1))

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