DenovoAsmAnnoT: Function for denovo Transcriptomics Assembly

In HTDA: HTDA (High Throughput Data Analysis)

Usage

DenovoAsmAnnoT(command, file1, file2, type, seqtype, ram, lib, cpu..)

Arguments

command	Full path where trinity installed
file1	In case of paired end file, this file will be the file which has all left read
file2	File with right reads
type	Paired or Single end reads
seqtype	Read format i.e. Paired or Single
ram	Availble ram
lib	Library used if strand specific reads
cpu..	number of processor

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (command, file1, file2, type, seqtype, ram, lib, cpu..) 
{
    command1 <- paste(command, "Trinity.pl", sep = "")
    if (type == "single") {
        command2 <- paste(command1, "--seqType", seqtype, "--JM", 
            ram, "--single", file1, "--SS_lib_type", lib, "--CPU", 
            cpu, "--no_cleanup", "--monitoring")
    }
    if (type == "single" & lib == "") {
        command2 <- paste(command1, "--seqType", seqtype, "--JM", 
            ram, "--single", file1, "--CPU", cpu, "--no_cleanup", 
            "--monitoring")
    }
    if (type == "paired") {
        command2 <- paste(command1, "--seqType", seqtype, "--JM", 
            ram, "--left", file1, "--right", file2, "--SS_lib_type", 
            lib, "--CPU", cpu, "--no_cleanup", "--monitoring")
    }
    if (type == "paired" & lib == "") {
        command2 <- paste(command1, "--seqType", seqtype, "--JM", 
            ram, "--left", file1, "--right", file2, "--CPU", 
            cpu, "--no_cleanup", "--monitoring")
    }
    system(command2)
    command3 <- paste(command, "util/TrinityStats.pl", sep = "")
    fasta <- "trinity_out_dir/Trinity.fasta"
    command4 <- paste(command3, fasta)
    AssembledStat <- system(command4, intern = TRUE)
    AssembledStat <- gsub("\t", "", AssembledStat)
    AssembledStat <- strsplit(AssembledStat, "\n")
    AssembledStat <- do.call(rbind.data.frame, AssembledStat)
    colnames(AssembledStat) <- "AssembledStat"
    com <- paste(command, "trinity-plugins/transdecoder/TransDecoder", 
        sep = "")
    com1 <- paste(com, "-t", fasta)
    system(com1)
    new("SequnecAnalysisData", AssembStat = AssembledStat)
  }

HTDA documentation built on May 2, 2019, 4:53 p.m.