WgetQC: Retrive data from GEO, and run a fastqc

In ZhenWei10/RbashGEO: GEO raw data processing in bash.

Usage

WgetQC(GEO_accession = "SRR1234567", Paired = F)

See Also

Rhisat2, Rtrim_galore ,and Coldata_example

Examples

library(RbashGEO)
library(dplyr)
Coldata_new <- read.csv("./Coldata_new.csv") #See attached collumn data example in Coldata_example

mapply(
  function(x,y){
    Rhisat2(Fastq_file_name = x,
            Paired = y,
            parallel_num = 1,
            Fastq_directory = getwd()) %>% Rnohup(.,paste0(x,"_hisat2"))}, 
  Coldata_new$SRR_RUN,
  (Coldata_new$Lib == "Paired")
)

ZhenWei10/RbashGEO documentation built on May 28, 2019, 8:22 a.m.