seismic-rna Logo
  • Why SEISMIC-RNA
    • What SEISMIC-RNA does
    • What distinguishes SEISMIC-RNA
    • Where to go next
  • How SEISMIC-RNA Works
    • FASTQ files
    • seismic align
    • seismic idmut
    • seismic filter
    • seismic cluster
    • seismic fold
  • Install
    • System Requirements
    • Option 1: Install with Conda, if you already know how to use it
    • Option 2: Install with Conda, if you don’t know how to use it
      • Step 1: Install Conda
      • Step 2: Create a Conda environment for SEISMIC-RNA
      • Step 3: Activate the Conda environment for SEISMIC-RNA
      • Step 4: Install SEISMIC-RNA and its dependencies
    • Option 3: Install with Conda, if conda install seismic-rna fails
    • Option 4: Install without Conda
    • Option 5: Update to another version of SEISMIC-RNA
      • Option 5A: Update SEISMIC-RNA to the latest stable version
      • Option 5B: Install a specific version of SEISMIC-RNA
    • Appendix 1: Install the dependencies of SEISMIC-RNA with or without Conda
    • Appendix 2: Install SEISMIC-RNA without Conda
      • Option 2A: Install SEISMIC-RNA from the Python Package Index
      • Option 2B: Install SEISMIC-RNA from GitHub
    • Appendix 3: Set the DATAPATH environment variable
    • Appendix 4: Test SEISMIC-RNA
      • Step 1: Run SEISMIC-RNA’s testing suite
      • Step 2: Interpret the test results
  • How to Use
    • seismic wf
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Caveats
      • Performance tips
      • Common errors
      • Common unexpected results
      • See also
    • seismic demult
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic align
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic idmut
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic pool
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic filter
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic cluster
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic join
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic filterscan
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic clusterscan
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic table
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic fold
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic graph
      • Purpose
      • Subcommands
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
        • Graph Results
    • seismic draw
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic collate
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic export
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic splitbam
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic cleanfa
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • seismic list
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic renumct
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic sim
      • Purpose
      • Subcommands
      • Quick example
      • See also
    • seismic importmm
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic ct2db
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic db2ct
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • See also
    • seismic migrate
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Caveats
      • Common errors
      • See also
    • seismic test
      • Purpose
      • Inputs
      • Outputs
      • Quick example
      • Options
      • Common unexpected results
      • See also
    • Specify Input Files
      • List files explicitly
      • Use glob patterns
      • Pass a directory
      • Combine methods
      • Glob patterns in options that accept multiple paths
    • Define Regions
      • Define a region by coordinates
      • Define a region by primer sequences
      • Define regions in a file
      • Multiple regions per reference
      • Region names
      • See also
    • Log Messages
      • Controlling terminal output
      • Log files
    • Parallelize Tasks
      • --num-cpus N
      • Batches
      • Recommendations
      • See also
    • Branches
      • How branches work
      • Which steps support --branch
      • See also
  • Tutorials
    • Tutorial 1: Amplicon prepared with RT-PCR
      • TL;DR
      • Scientific premise
      • Download example files of an amplicon
      • Process the no-DMS control
        • Run the workflow on the no-DMS control
        • Check the graphs of coverage and mutation rate for the no-DMS control
        • Mask out the position that is highly mutated in the no-DMS sample
      • Process both DMS-modified replicates
        • Run the workflow on both DMS-treated replicates
        • Check the correlation of mutation rates between DMS-treated replicates
      • Pool the DMS-treated replicates and process them together
        • Pool the two DMS-treated replicates
        • Process the pooled DMS-treated samples
        • Check whether the RNA forms alternative structures
        • Draw the best-supported structure model for each cluster
    • Tutorial 2: Running a sample with a single-end FASTQ
      • Download example file
      • Run the SEISMIC-RNA workflow
      • Output
    • Tutorial 3: Clustering
      • Download example file
      • Run the SEISMIC-RNA workflow
      • Output
      • Further analysis
    • Tutorial 4: Running multiple samples at once
      • Download example files
      • Run the SEISMIC-RNA workflow
      • Output
    • Tutorial 5: Masking using a regions file
      • Download example files
      • Run the SEISMIC-RNA workflow
      • Output
  • Bugs and Requests
    • How to give feedback
      • Guidelines for reporting bugs and other problems
      • Guidelines for requesting new features and other enhancements
  • How to Cite
    • Citing SEISMIC-RNA
    • Authors
    • License
    • DMS-MaPseq
  • Command Line Reference
    • Run the entire workflow
      • seismic wf
    • Run individual steps of the workflow
      • seismic demult
      • seismic align
      • seismic idmut
      • seismic pool
      • seismic filter
      • seismic cluster
      • seismic join
      • seismic filterscan
      • seismic clusterscan
      • seismic table
      • seismic fold
      • seismic graph
        • seismic graph profile
        • seismic graph delprof
        • seismic graph scatter
        • seismic graph corroll
        • seismic graph giniroll
        • seismic graph snrroll
        • seismic graph histpos
        • seismic graph histread
        • seismic graph mutdist
        • seismic graph poscorr
        • seismic graph roc
        • seismic graph aucroll
        • seismic graph abundance
        • seismic draw
        • seismic collate
        • seismic export
    • Utility commands
      • seismic splitbam
      • seismic cleanfa
      • seismic list
      • seismic renumct
      • seismic ct2db
      • seismic db2ct
      • seismic importmm
      • seismic migrate
      • seismic fold datapath
      • seismic test
      • seismic sim
        • seismic sim total
        • seismic sim ref
        • seismic sim fold
        • seismic sim params
        • seismic sim muts
        • seismic sim ends
        • seismic sim clusts
        • seismic sim idmut
        • seismic sim fastq
        • seismic sim abstract
  • API Reference
    • seismicrna package
      • Subpackages
        • seismicrna.align package
        • seismicrna.cleanfa package
        • seismicrna.cluster package
        • seismicrna.clusterscan package
        • seismicrna.collate package
        • seismicrna.core package
        • seismicrna.demult package
        • seismicrna.draw package
        • seismicrna.export package
        • seismicrna.filter package
        • seismicrna.filterscan package
        • seismicrna.fold package
        • seismicrna.graph package
        • seismicrna.idmut package
        • seismicrna.importmm package
        • seismicrna.renumct package
        • seismicrna.sim package
        • seismicrna.test package
        • seismicrna.tests package
      • Submodules
        • dataset_from_report()
        • table_from_dataset()
        • table_from_report()
        • join_regions()
        • joined_filter_report_exists()
        • parse_join_clusts_file()
        • run()
        • write_report()
        • find_pos()
        • iter_tables()
        • run()
        • write_list()
        • compute_arc_points()
        • draw_seismic_logo()
        • migrate_out_dir()
        • migrate_sample_dir()
        • run()
        • pool_samples()
        • run()
        • write_report()
        • get_dataset_flags()
        • get_tabulator_type()
        • load_all_datasets()
        • run()
        • tabulate()
        • open_url()
        • flatten()
        • run()
  • File Formats
    • Data Formats
      • FASTA: Reference sequences
        • FASTA file: Content format
        • FASTA file: Path format
        • FASTA file: Uses
      • FASTQ: Sequencing Reads
        • FASTQ file: Content format
        • FASTQ file: Path format
        • FASTQ file: Uses
      • SAM, BAM, and CRAM: Alignment Maps
        • XAM file: Content format
        • XAM file: Path format
        • XAM file: Uses
      • Brickle: Compressed Python Objects
        • Brickle file: Content format
        • Brickle file: Path format
        • Brickle file: Uses
      • Connectivity Table (CT): RNA secondary structures
        • CT file: Content format
        • CT file: Path format
        • CT file: Uses
      • Dot-bracket (DB): RNA secondary structures
        • DB file: Content format
        • DB file: Path format
        • DB file: Uses
      • VARNA Color: Color codes for VARNA
        • VARNA color file: Content format
        • VARNA color file: Path format
        • VARNA color file: Uses
      • Sample results: Export data from SEISMIC-RNA to SEISMIC-GRAPH
        • Sample results: Content format
        • Sample results file: Path format
        • Sample results file: Uses
    • List Formats
      • List of Positions
        • List of Positions: Fields
        • List of Positions file: Uses
        • Example List of Positions
    • Metadata Formats
      • Metadata for Samples
        • About metadata for samples
        • Fields of metadata for samples
        • Example metadata for samples
      • Metadata for References
        • About metadata for references
        • Fields of metadata for references
        • Example metadata for references
      • Metadata for Regions
        • About metadata for regions
        • Fields of metadata for regions
        • Example metadata for regions
      • Metadata for Joined Clusters
        • About metadata for joined clusters
        • Fields of metadata for joined clusters
        • Example metadata for joined clusters
    • Report Formats
      • Align Report
        • Align Sample Report
        • Align Reference Report
      • IDmut Report
        • IDmut Report: Fields
        • IDmut Report: Example
      • Pool Report
        • Pool Report: Fields
        • Pool Report: Example
      • Filter Report
        • Filter Report: Fields
        • Filter Report: Example
      • Filterscan Report
        • Filterscan Report: Fields
        • Filterscan Report: Example
      • Cluster Report
        • Cluster Report: Fields
        • Cluster Report: Example
      • Clusterscan Report
        • Clusterscan Report: Fields
        • Clusterscan Report: Example
      • Join Report
        • Join Filter Report
        • Join Cluster Report
      • Fold Report
        • Fold Report: Fields
        • Fold Report: Example
  • Data Structures
    • IDmut Data Structures
      • Relation Vectors
        • Relationships between reads and references
        • Encoding primary relationships
        • Encoding ambiguous relationships
        • Encoding positions not covered by the read
        • Encoding paired-end reads
      • IDmut Batch
        • IDmut batch: Structure
        • IDmut batch: Example
      • Read Names Batch
        • Read names batch: Structure
        • Read names batch: Example
      • Reference Sequence
        • Reference sequence: Structure
        • Reference sequence: Example
  • Algorithms
    • Algorithm for Finding Ambiguous Insertions and Deletions
      • Background on Ambiguous Insertions and Deletions
        • Why this matters
        • Goal of the algorithm
      • How the Algorithm Works
        • Sliding an indel
        • Keeping indels of different kinds separate
        • The two sliding passes
        • Checks made before each move
        • A note on insertions
      • Example
    • Algorithm for Sequence Compression/Decompression
      • Background on Sequence Compression/Decompression
      • Algorithm for Sequence Compression
        • Algorithm for Sequence Compression: Procedure
        • Algorithm for Sequence Compression: Example
      • Algorithm for Sequence Decompression
        • Algorithm for Sequence Decompression: Procedure
        • Algorithm for Sequence Decompression: Example
    • Normalize Mutation Rates
      • How to normalize mutation rates to a quantile
  • FAQs
    • Installation and external tools
      • Why does seismic fold fail with a DATAPATH error?
      • Why does seismic draw print “Skip draw if RNARTISTCORE is not installed”?
      • Which optional dependencies do I actually need?
    • Renamed commands and options (v0.25.0)
    • Probes and probe-specific defaults
      • What does --probe do?
      • When should I set --probe none?
    • Performance and parallelism
      • How do I make seismic wf run faster?
      • How do I limit memory usage?
    • Output and interpretation
      • Where do my output files go?
      • Why is my output empty / why were all my reads filtered out?
      • I ran seismic wf but got no structures / no clustered output / no JSON.
      • How do I re-run only one step?
    • Troubleshooting and support
      • How do I see what SEISMIC-RNA is actually doing?
      • I found a bug. Where do I report it?
      • I have a question that’s not answered here.
seismic-rna
  • How to Use
  • seismic graph
  • Graph Results
  • View page source

Graph Results

Like seismic itself, seismic graph has several subcommands, with which you can make a variety of graphs.

  • Profile: Bar graph of relationships(s) per position
    • Profile: Input files
    • Profile: Settings
    • Profile: Output files
    • Profile: Examples
  • General parameters for graphing
    • General parameters for graphing: Input files
    • General parameters for graphing: Input data
    • General parameters for graphing: Output files
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