Rhisat2: Generate hisat2 command in R

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

Usage

Rhisat2(Fastq_file_name = "SRR1234567",
  indx_directory = "/home/zhen/hisat2_idx/hg19/genome",
  Fastq_directory = ".", Paired = F, trim_5 = NULL, trim_3 = NULL,
  parallel_num = 8, Fastq_file_end = ".fastq",
  output_name = Fastq_file_name, tune_Mismatch_MX = NULL,
  tune_Mismatch_MN = NULL)

See Also

Check_hisat2_reports

Examples

library(RbashGEO)
library(dplyr)
Coldata_new <- read.csv("./Coldata_M14new.csv")

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.