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

Select Genome Assembly

It is a simple step. You can simply select Genome assembly used in the RNA-seq experiment. rMAPS currently supports human (hg38, hg19), mouse (mm10), fly (dm6, dm3), rat (rn6), C. elegans (ce11), zebrafish (danRer10, danRer11), Arabidopsis thaliana (araTha1), frog (xenLae2, xenTro9), and rice (oSa7) are available.

Upload Your Differential Alternative Splicing Output Data

rMAPS supports rMATS outputs, miso outputs, and user-provided coordinates for differential alternative splicing exons and control exons. rMAPS can analyze all 5 major types of alternative splicing events as follows:
            Skipped Exon (SE)
            Mutually eXclusive Exon (MXE)
            Alternative to 5′ Splice Site (A5SS)
            Alternative to 3′ Splice Site (A3SS)
            Retained Intron (RI)

     using rMATS outputs:
  1. Upload rMATS output (simple and recommended).
    1. Run rMATS program (computational tool to detect differential alternative splicing events).
    2. Save output files from the rMATS run.
  2. Click on “upload” then select files for alternative splicing events that you are interested in:
rMATS output file could be
rMATS SE output  (SE.MATS.ReadsOnTargetAndJunctionCounts.txt)
rMATS MXE output  (MXE.MATS.ReadsOnTargetAndJunctionCounts.txt)
rMATS A5SS output  (A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt)
rMATS A3SS output  (A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt)
rMATS RI output  (RI.MATS.ReadsOnTargetAndJunctionCounts.txt)
     using MISO outputs:
  1. Upload MISO output.
    1. Run MISO program (computational tool to detect differential alternative splicing events).
    2. Save output files from the MISO run.
  2. Click on “upload” then select files for alternative splicing events that you are interested in:
using User-provided coordinates:
  1. Upload coordinates manually.
    1. Provide coordinates of upregulated exons, downregulated exons, background exons for alternative splicing events that you are interested in:
User provided input format

[ User input format for SE event ]



Exon coordinates are from three exons involved in skipping events.



[ User input format for MXE event ]



Exon coordinates are from four exons involved in mutually exclusive events.

[ User input format for A5SS event ]



Exon coordinates are from three exons involved in alternative to 5′ splicing events.

[ User input format for A3SS event ]



Exon coordinates are from three exons involved in alternative to 3′ splicing events.

[ User input format for RI event ]



Exon coordinates are from three exons involved in retained intron events.

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
Click on “Run” button to get motif enrichment analysis plots.

          It typically takes under 4 minutes for all 5 alternative splicing types together.

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

[ rMAPS Output example for SE event ]
[ rMAPS Output example for RI event ]
[ rMAPS Output example for A5SS event ]
[ rMAPS Output example for A3SS event ]
[ rMAPS Output example for MXE event ]

Running CLIP Map

Upload Your Differential Alternative Splicing Output Data

  1. Upload rMATS output (simple and recommended).
    1. Run rMATS program (computational tool to detect differential alternative splicing events).
    2. Save output files from the rMATS run.
    3. Click on “upload” then select files for alternative splicing events that you are interested in:
Upload Peak Caller output (bed format).

  1. Run CLIP-seq peak caller program. rMAPS was tested with Piranha and PIPE-CLIP.
  2. Save output files from the peak caller run.
  3. Click on “Choose File”, then select the peak caller file
  4. Click on “Upload” in order to transfer the peak caller file as input
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
Click on “Run” button get RNA-map analysis plots.

          It typically takes under 1 minute for all 5 alternative splicing types together.

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.
CLIP Map Output

[ rMAPS Output example for SE event ]
[ rMAPS Output example for RI event ]
[ rMAPS Output example for A5SS event ]
[ rMAPS Output example for A3SS event ]
[ rMAPS Output example for MXE event ]