NAME

       rsem-plot-transcript-wiggles - Generate PDF wiggle plots from transcript or gene ids

SYNOPSIS

        rsem-plot-transcript-wiggles [options] sample_name input_list output_plot_file

ARGUMENTS

       sample_name
           The name of the sample analyzed.

       input_list
           A list of transcript ids or gene ids. But it cannot be a mixture of transcript & gene
           ids. Each id occupies one line without extra spaces.

       output_plot_file
           The file name of the pdf file which contains all plots.

OPTIONS

       --gene-list
           The input-list is a list of gene ids. (Default: off)

       --transcript-list
           The input-list is a list of transcript ids. This option can only be turned on if
           allele-specific expression is calculated. (Default: off)

       --show-unique
           Show the wiggle plots as stacked bar plots. See description section for details.
           (Default: off)

       -p/--num-threads <int>
           Set the number of threads we can use. (Default: 1)

       --memory-per-thread <string>
           Set the maximum allowable memory per thread. <string> represents the memory and
           accepts suffices 'K/M/G'. (Default: 1G)

       -h/--help
           Show help information.

DESCRIPTION

       This program generates transcript wiggle plots and outputs them in a pdf file. This
       program can accept either a list of transcript ids or gene ids (if transcript to gene
       mapping information is provided) and has two modes of showing wiggle plots. If
       '--show-unique' is not specified, the wiggle plot for each transcript is a histogram where
       each position has the expected read depth at this position as its height. If
       '--show-unique' is specified, for each transcript a stacked bar plot is generated. For
       each position, the read depth of unique reads, which have only one alignment, is showed in
       black. The read depth of multi-reads, which align to more than one places, is showed in
       red on top of the read depth of unique reads.This program will use some files RSEM
       generated previouslly. So please do not delete/move any file 'rsem-calculate-expression'
       generated. If allele-specific expression is calculated, the basic unit for plotting is an
       allele-specific transcript and plots can be grouped by either transcript ids
       (--transcript-list) or gene ids (--gene-list).

OUTPUT

       output_plot_file
           This is a pdf file containing all plots generated. If a list of transcript ids is
           provided, each page display at most 6 plots in 3 rows and 2 columns. If gene ids are
           provided, each page display a gene. The gene's id is showed at the top and all its
           transcripts' wiggle plots are showed in this page. The arrangement of plots is
           determined automatically. For each transcript wiggle plot, the transcript id is
           displayed as title. x-axis is position in the transcript and y-axis is read depth. If
           allele-specific expression is calculated, the basin unit becomes an allele-specific
           transcript and transcript ids and gene ids can be used to group allele-specific
           transcripts.

       sample_name.transcript.sorted.bam and sample_name.transcript.readdepth
           If these files do not exist, 'rsem-plot-transcript-wiggles' will automatically
           generate them.

       sample_name.uniq.transcript.bam, sample_name.uniq.transcript.sorted.bam and
       sample_name.uniq.transcript.readdepth
           If '--show-unique' option is specified and these files do not exist,
           'rsem-plot-transcript-wiggles' will automatically generate them.

EXAMPLES

       Suppose sample_name and output_plot_file are set to 'mmliver_single_quals' and
       'output.pdf' respectively. input_list is set to 'transcript_ids.txt' if transcript ids are
       provided, and is set to 'gene_ids.txt' if gene ids are provided.

       1) Transcript ids are provided and we just want normal wiggle plots:

        rsem-plot-transcript-wiggles mmliver_single_quals transcript_ids.txt output.pdf

       2) Gene ids are provided and we want to show stacked bar plots:

        rsem-plot-transcript-wiggles --gene-list --show-unique mmliver_single_quals gene_ids.txt output.pdf