File dello script

(base) [genomica@localhost RSEM]$ sudo ./rsem-generate-ngvector
Invalid number of arguments!
NAME
    rsem-generate-ngvector - Create Ng vector for EBSeq based only on
    transcript sequences.

SYNOPSIS
    rsem-generate-ngvector [options] input_fasta_file output_name

ARGUMENTS
    input_fasta_file
        The fasta file containing all reference transcripts. The transcripts
        must be in the same order as those in expression value files. Thus,
        'reference_name.transcripts.fa' generated by
        'rsem-prepare-reference' should be used.

    output_name
        The name of all output files. The Ng vector will be stored as
        'output_name.ngvec'.

OPTIONS
    -k <int>
        k mer length. See description section. (Default: 25)

    -h/--help
        Show help information.

DESCRIPTION
    This program generates the Ng vector required by EBSeq for isoform level
    differential expression analysis based on reference sequences only.
    EBSeq can take variance due to read mapping ambiguity into consideration
    by grouping isoforms with parent gene's number of isoforms. However, for
    de novo assembled transcriptome, it is hard to obtain an accurate
    gene-isoform relationship. Instead, this program groups isoforms by
    using measures on read mappaing ambiguity directly. First, it calculates
    the 'unmappability' of each transcript. The 'unmappability' of a
    transcript is the ratio between the number of k mers with at least one
    perfect match to other transcripts and the total number of k mers of
    this transcript, where k is a parameter. Then, Ng vector is generated by
    applying Kmeans algorithm to the 'unmappability' values with number of
    clusters set as 3. 'rsem-generate-ngvector' will make sure the mean
    'unmappability' scores for clusters are in ascending order. All
    transcripts whose lengths are less than k are assigned to cluster 3.

    If your reference is a de novo assembled transcript set, you should run
    'rsem-generate-ngvector' first. Then load the resulting
    'output_name.ngvec' into R. For example, you can use

     NgVec <- scan(file="output_name.ngvec", what=0, sep="\n")

    . After that, replace 'IsoNgTrun' with 'NgVec' in the second line of
    section 3.2.5 (Page 10) of EBSeq's vignette:

     IsoEBres=EBTest(Data=IsoMat, NgVector=NgVec, ...)

    This program only needs to run once per RSEM reference.

OUTPUT
    output_name.ump
        'unmappability' scores for each transcript. This file contains two
        columns. The first column is transcript name and the second column
        is 'unmappability' score.

    output_name.ngvec
        Ng vector generated by this program.

EXAMPLES
    Suppose the reference sequences file is
    '/ref/mouse_125/mouse_125.transcripts.fa' and we set the output_name as
    'mouse_125':

     rsem-generate-ngvector /ref/mouse_125/mouse_125.transcripts.fa mouse_125