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41
Documentation / HTMLSummary
« Last post by xiangjun on September 27, 2016, 02:51:44 pm »
Following a MatrixREDUCE or MotifREDUCE run, a bunch of output files (model parameters, PSAMs etc.) are generated. The HTMLSummary utility program is provided to summarize the main results in a intuitive, easy to follow HTML page so that (even non-expert) users can quickly make sense of their findings, e.g., the top list of significant PSAMs (motifs). Internally, HTMLSummary makes system-calls to the utility program LogoGenerator to create the logo images. These inter-connected programs, plus a few others, constitute the REDUCE Suite.

HTMLSummary [options] [-file=HTMLFile]

  Required parameters:
    none

  Optional parameters:
    [-output=dir_name]  --- path to an MatrixREDUCE/MotifREDUCE run directory,
                            used both as input and output for HTML summary (./)
    [-copy]             --- copy CSS, JavsScript and associated image files to
                            the output directory to make the HTML self-contained
    [-rc]               --- logo based on reverse complementary strand
    [-width=ThumbnailImageWidthInPixel]   (145)
    [-height=ThumbnailImageHeightInPixel] (90)
    [-psam_list=list_of_PSAMs] --- generate a summary LOGO page for the list
                                   of PSAMs in the file
    [-file=HTMLFile]    --- HTML output file name (index.html)

  Usage: (following a MatrixREDUCE run)
    HTMLSummary
    HTMLSummary -psam=psams.list -file=psams.html
42
Documentation / MatrixREDUCE
« Last post by xiangjun on September 27, 2016, 02:43:34 pm »
MatrixREDUCE uses genome-wide occupancy data for a transcription factor (e.g. ChIP-chip or mRNA expression data) and associated nucleotide sequences to discover the sequence-specific binding affinity of the transcription factor. The sequence specificity of the transcription factor's DNA-binding domain is modeled using a position-specific affinity matrix (PSAM), representing the change in the binding affinity (Kd) whenever a specific position within a reference binding sequence is mutated.

MatrixREDUCE [options] -sequence=seqfile -measurement=measfile

  Required parameters:
    -sequence=seqfile     --- sequence file in FASTA format
    -meas=measfile        --- measurement (expression/binding) file in tab-delimited format

  Optional parameters:
    [-topo_list=topofile]  --- name of topology file (up_to_octamers)
    [-topo=topology]       --- single topology pattern, e.g., X3--X4
    [-multifit]            --- switch to seed/optimize using all experiments
                                   [added based on code from Pilar -- thanks!]
    [-dicfile=file]        --- list of motifs to check against. IUPAC wild cards
                                   allowed; no length limit
    [-ntop=integer]        --- number of top seed motifs to print out (10)
    [-iupac_pos=integer]   --- number of positions to check for IUPAC degeneracy (0)
    [-iupac_sym=string]    --- IUPAC symbols to check against ('KMRSWYBDHVN')

    [-output=dir_name]     --- path to the output directory (./)
    [-p_value=float]       --- threshold to stop looking for new PSAMs (0.001)
    [-max_motif=integer]   --- maximum # of PSAMs to search (20)
    [-strand=integer]      ---  1 |+1 |F | L for leading strand;
                                2 |+2 |B     for both strands;
                               -1 | R |C     for reverse complementary;
                                0 | A |D     auto-detection (check 1 and 2)

    [-runlog=[stderr|stdout|file]]
                           --- direct running diagnostics message to stderr,
                                   stdout or a specific file (stderr)
    [-help]                --- print out this help message

  Usages:
    mkdir -p results
    MatrixREDUCE \
       -meas=$REDUCE_SUITE/data/mRNA_expression/Spellman1998AlphaTimeCourse.tsv \
       -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
       -topo_list=$REDUCE_SUITE/data/topology/up_to_octamers -o=results
    HTMLSummary -o=results

    mkdir -p X6
    MatrixREDUCE \
       -meas=$REDUCE_SUITE/data/mRNA_expression/Spellman1998AlphaTimeCourse.tsv \
       -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
       -topo=X6 -o=X6
    HTMLSummary -c -o=X6

43
Documentation / MotifREDUCE
« Last post by xiangjun on September 27, 2016, 02:39:42 pm »
REDUCE is an acronym that stands for Regulatory Element Detection Using Correlation with Expression. Based on a simple model for transcriptional regulation by independently acting transcription factors, REDUCE makes it possible to find regulatory elements based on a single microarray experiment. MotifREDUCE in the REDUCE Suite is a more robust and efficient reimplementation of the "original REDUCE algorithm" by Bussemaker et al (2001).

MotifREDUCE [options] -sequence=seqfile -measurement=measfile

  Required parameters:
    -sequence=seqfile     --- sequence file in FASTA format
    -meas=measfile        --- measurement (expression/binding) file in tab-delimited format

  Optional parameters:
    [-topo_list=topofile]  --- name of topology file (up_to_octamers)
    [-topo=topology]       --- single topology pattern, e.g., X3--X4
    [-dicfile=file]        --- list of motifs to check against. IUPAC wild cards
                                   allowed; no length limit
    [-ntop=integer]        --- number of top seed motifs to print out (10)
    [-iupac_pos=integer]   --- number of positions to check for IUPAC degeneracy (0)
    [-iupac_sym=string]    --- IUPAC symbols to check against ('KMRSWYBDHVN')

    [-output=dir_name]     --- path to the output directory (./)
    [-p_value=float]       --- threshold to stop looking for new motifs (0.001)
    [-max_motif=integer]   --- maximum # of motifs to search (20)
    [-strand=integer]      ---  1 |+1 |F | L for leading strand;
                                2 |+2 |B     for both strands;
                               -1 | R |C     for reverse complementary;
                                0 | A |D     auto-detection (check 1 and 2)

    [-runlog=[stderr|stdout|file]]
                           --- direct running diagnostics message to stderr,
                                   stdout or a specific file (stderr)
    [-help]                --- print out this help message

  Usage:
    mkdir -p results   # use topology file (up_to_heptamers)
    MotifREDUCE \
        -meas=$REDUCE_SUITE/examples/MotifREDUCE/yeast_sample.csv \
        -sequence=$REDUCE_SUITE/examples/MotifREDUCE/genome5pns600.fasta \
        -topo_list=$REDUCE_SUITE/examples/MotifREDUCE/up_to_heptamers \
        -o=results
    HTMLSummary -c -o=results

Notes:
  • The command-line user-interface of MotifREDUCE is identical to that of MatrixREDUCE, but skips the Levenberg-Marquardt non-linear least-squares optimization of weight matrix (Ws). The result is a list of motifs, which are expressed in matrix form with 1s and 0s.
  • The above example dataset takes ~10s and finds 10 significant motifs on a contemporary laptop computer.
44
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by knie on September 27, 2016, 02:01:22 am »
Hi Xiang-Jun,

Got it! And thanks a lot for the information about logo colors :D

Best,
Kate
45
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by xiangjun on September 26, 2016, 11:18:16 pm »
Hi Kate,

Yes. You need to edit file $REDUCE_SUITE/html/LogoGenerator_PS.def slightly, as shown below.

Current (default settings):
Code: [Select]
/colorDict <<
    (A) green       (a) m_green
    (C) blue        (c) m_blue
    (G) orange      (g) m_orange
    (T) red         (t) m_red
    (U) cyan        (u) m_cyan
    (X) white
>> def

Change (U) cyan to (U) red will achieve what you asked. Of course, you can completely redefine the coloring scheme as you see fit in section "default color set".

A bit background info for the default colors: the A green, C blue, G orange, and T red coloring scheme follows WebLogo for DNA. On the other hand, the 3DNA software for 3D structures of DNA/RNA uses another convention: A red, C yellow, G green, T blue, and U cyan. See http://x3dna.org/articles/seeing-is-understanding-as-well-as-believing for some examples. So I ended up with cyan for U in RNA logo. Moreover, the REDUCE Suite Forum is based on the 3DNA Forum.

Best regards,

Xiang-Jun
46
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by knie on September 26, 2016, 06:03:44 pm »
Hi Xiang-Jun,

As a followup question:
The default color of the nucleotide "U" from `LogoGenerator -rna` is light blue. Is it possible to change it to red (like the color of "T" in DNA logos)?

Best,
Kate
47
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by knie on September 22, 2016, 03:31:21 pm »
Hi Xiangjun,

Perfect! Many thanks for the prompt reply.

Best,
Kate
48
General Discussion / Re: Generate RNA logos with LogoGenerator
« Last post by xiangjun on September 22, 2016, 10:29:37 am »
Hi Kate,

Thanks for using the REDUCE Suite and for posting your question on the Forum.

Yes, LogoGenerator is applicable to RNA as well as DNA. You just need to specify an additional -rna option on the command-line, and everything else should work as expected. Please have a try and report back any issues you may have.

Best regards,

Xiang-Jun


PS. The REDUCE Suite has more features than those documented (with the command-line "-h" option). The default settings are designed to work for its advertised purpose only.
49
General Discussion / Generate RNA logos with LogoGenerator
« Last post by knie on September 22, 2016, 06:36:17 am »
Hi,

Is it possible to generate RNA logos with LogoGenerator? (i.e., display U instead of T)

TIA.
Kate
50
General Discussion / Re: Defining Color in LogoGenerator
« Last post by xiangjun on August 11, 2016, 01:40:58 pm »
Hi,

Thanks for being the first to ask questions on the Forum! I'd like to clarify that the LogoGenerator utility is within the REDUCE Suite, which is a completely separate package from FeatureReduce.

As to your question of coloring some Cs (or other bases) in separately color, the answer is no, at least in the current version of LogoGenerator. The DNA/RNA logos, as I am aware of, consist of 4 different bases, as shown in the 4 columns of a PWM or PSAM. To color certain bases differently, such info must be specified in some way in the file, which will break the format.

There are so many logo generators available. Maybe some of them are more advanced than the functionality LogoGenerator currently provides, and can do what you are asking for.

If you want to generate only a fews logos, you could use LogoGenerator to generate the logos in EPS format. Then using Adobe Illustrator, you can edit/modify as you see fit.

Hope this helps.

Xiang-Jun

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also http://forum.x3dna.org and http://x3dna.org