QualityDenovo: Function to check the quality of the assembled Transcriptome
In HTDA: HTDA (High Throughput Data Analysis)

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

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

`path`	Full path where Trinity installed
`file`	Newly assembled transcriptome i.e. Trinity.fasta
`blastdb`	blast databse :- Genome database
`lib`
`..`

##---- 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)
  }