QualityDenovo: Function to check the quality of the assembled Transcriptome

Description Usage Arguments Examples

View source: R/QualityDenovo.R

Description

This function Align the assemble transcript with the genome(if available) by using BLAT. Also, align the reads with the newly assembled transcriptome, the resulting BAM files can be visualize by using IGB/IGB

Usage

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QualityDenovo(path, file, blastdb, lib, ..)

Arguments

path

Full path where Trinity installed

file

Newly assembled transcriptome i.e. Trinity.fasta

blastdb

blast databse :- Genome database

lib
..

Examples

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##---- 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 (path, file, blastdb, lib, ..) 
{
    out <- paste(file, "_blat", sep = "")
    command2 <- paste("blat", blastdb, file, "-t=dna -q=dna -out=blast8", 
        out)
    system(command2)
    command3 <- paste(path, "util/analyze_blastPlus_topHit_coverage.pl", 
        sep = "")
    command4 <- paste(command3, out, file, blastdb)
    AssemblesStat <- system(command4, intern = TRUE)
    command5 <- paste(path, "util/alignReads.pl", sep = "")
    command6 <- paste(command5, "--left", file1, "--right", file2, 
        "--seqType", seqtype, "--target", file, "--SS_lib_type", 
        lib, "--aligner bowtie --retain_intermediate_files")
    system(command6)
    command7 <- paste(path, "/sw/opt/trinity/util/SAM_nameSorted_to_uniq_count_stats.pl", 
        sep = "")
    command8 <- paste(command7, "bowtie_out/bowtie_out.nameSorted.sam")
    alignSummar <- system(command8, intern = TRUE)
  }

HTDA documentation built on May 31, 2017, 2:29 a.m.