Description Usage Arguments Details Value Examples
install in .local/bin using 'pip install –user –upgrade cutadapt'.
1 2 | run_cutadapt(inputdf, ad1 = "AGATCGGAAGAGC", ad2 = "AGATCGGAAGAGC",
q = 20, email = NULL, runinfo = c(FALSE, "bigmemh", 1))
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inputdf |
Data.frame with fq1, fq2, out1, out2, and report columns. Both input and output can be gzipped (.gz). |
ad1 |
Adapter 3' method, see cutadapt documentation for more details. Same for ad2. |
q |
quality_cutoff 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 |
For more information: https://cutadapt.readthedocs.io/en/stable/index.html version: v1.10
return A batch of shell scripts.
1 2 3 4 5 | fqs <- c("$HOME/dbcenter/Ecoli/fastq/SRR2921970.sra_1.fastq.gz",
"$HOME/dbcenter/Ecoli/fastq/SRR2921970.sra_2.fastq.gz")
inputdf <- data.frame(fq1=fqs[1], fq2=fqs[2], out1=fqs[1], out2=fqs[2])
run_cutadapt(inputdf, ad1="AGATCGGAAGAGC", ad2="AGATCGGAAGAGC", q=20,
email=NULL, runinfo = c(FALSE, "bigmemh", 1))
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