plotEnrichment (version 3.5.4+galaxy0)

Sample order matters:

By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.

BAM/CRAM file:

Would you like custom sample labels?:

By default, the names of the samples in your history are used.

Regions in BED/GTF format:

One or more files containing regions to include in the analysis

Region of the genome to limit the operation to:

This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".

Image file format:

Note that the plotly output can be very large and not all options are supported.

Show advanced options:

Save percentages to a file:

What it does

This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed.

Output

The output file is a plot in the format specified. A table of the percentages and raw counts can also be created.

For more information on the tools, please visit our help site.

For support or questions please post to Biostars. For bug reports and feature requests please open an issue on github.

This tool is developed by the Bioinformatics and Deep-Sequencing Unit at the Max Planck Institute for Immunobiology and Epigenetics.