User Guide



Running rMAPS

rMAPS consists of two tools. Motif Map performs motif enrichment analysis for RNA-binding proteins. CLIP Map examines CLIP-seq peak data to generate RNA-map of the protein used in the CLIP-seq experiment.



Running Motif Map

  1. Select Genome Assembly

    It is a simple step. You can simply select Genome assembly used in the RNA-seq experiment.
    Currently, hg38, hg19, mm10, dm6, dm3, rn6, ce11, and danRer10 are available.

  2. Upload rMATS SE output, SE.miso_bf output, or provide your own coordinates for differential alternative splicing exons and control exons.
    1. Upload rMATS output (simple and recommended).
      1. Run rMATS program (computational tool to detect differential alternative splicing events).
      2. Save SE.MATS.ReadsOnTargetAndJunctionCounts.txt file from the rMATS run.
      3. Click on “upload” then select SE.MATS.ReadsOnTargetAndJunctionCounts.txt file
        (uploading could take ~1 minute).
    2. Upload coordinates manually.
      1. Provide coordinates of “upregulated, downregulated, and background” exons in the following format.
      2. Exon coordinates are from three exons involved in skipping events.
  3. Enter “Optional Parameters”.
    1. Intron (default 250): Length of the intronic region to be examined and plotted.
    2. Exon (default 50): Length of the exonic region to be examined and plotted.
    3. Sliding Window Size (default 50): Size of the sliding window to be used to count the motif occurrences.
    4. Interval (default 1): Step size of windows sliding.
    5. Additional Motif (no default value): User input of Motif
        rMAPS takes optional motifs from users with flexibility provided by the regular expressions.
        Here are some useful regular expressions with examples.

        Multiple regular expressions can be used at the same time.
        For example, [TG]TGG[GC]T would look for 4 patterns
        (i.e., TTGGGT or TTGGCT or GTGGGT or GTGGCT)
    6. Email (no default value): An option to send a link of the result via email
  4. Click on “Run” button to get motif enrichment analysis plots.
    1. It typically takes ~10 minutes.
  5. Examine output plots and folder.
    1. rMAPS gives a link to output folder which will be accessible for 48 hours.
    2. rMAPS also provides links to each plot in both PDF format and PNG format.


MOTIF Map Output





Running CLIP Map

  1. Upload rMATS SE output, SE.miso_bf output, or provide your own coordinates for differential alternative splicing exons and control exons.
    1. Upload rMATS output (simple and recommended).
      1. Run rMATS program (computational tool to detect differential alternative splicing events).
      2. Save SE.MATS.ReadsOnTargetAndJunctionCounts.txt file from the rMATS run.
      3. Click on rMATS SE output “upload” button
        then select SE.MATS.ReadsOnTargetAndJunctionCounts.txt file
        (uploading could take ~1 minute).
    2. Upload coordinates manually.
      1. Provide coordinates of “upregulated, downregulated, and background” exons.
  2. Upload Peak Caller output (bed format).
    1. Run CLIP-seq peak caller. rMAPS was tested with Piranha and PIPE-CLIP.
    2. Click on Peak Caller Output “upload” button
      then select the peak caller output file in bed format.
      It could take more than 5 minutes depending on the peak caller output size.
  3. Enter “Optional Parameters”.
    1. RBP Name (default Protein): Enter the name of the protein used in CLIP-seq experiment.
    2. Intron (default 250): Length of the intronic region to be examined and plotted.
    3. Exon (default 50): Length of the exonic region to be examined and plotted.
    4. Sliding Window Size (default 50): Size of the sliding window to be used to count the motif occurrences.
    5. Interval (default 1): Step size of windows sliding.
    6. Email (no default value): An option to send a link of the output result via email
  4. Click on “Run” button to get RNA-map analysis plots.
    1. It typically takes ~5 minutes.
  5. Examine output plot and folder.
    1. rMAPS gives a link to output folder which will be accessible for 48 hours.
    2. rMAPS also provides links to the RNA-map in both PDF format and PNG format.


CLIP Map Output