Visualizing FIMO Output

Question

[gordian.knot0]

Long time lurker, first time poster. Appreciate all of the help I have been able to get from reading through this community!

My particular problem: I have a list of RNA sequences that I looked for my favourite motif using FIMO. This gave me the expected output, a list of coordinates where my favourite motif is found in my list of RNA sequences. I now wish to visualize this by essentially representing my RNA sequences as black lines based on length, and then somehow use block diagrams to depict the location of my favourite motif throughout these sequences. Does anyone know of a software or a program? I know MEME suite has a motif localization plot, but it's not quite publication quality.

Thank you everyone for your insight!

Answer 1

[Alex Reynolds]

You could use awk to easily reformat the BED output for your RNA reads and TSV-formatted motif hits into UCSC BED12, using different colors and metadata for each category.

Then bring your BED12 files into the UCSC Genome Browser and set up a personal session, so that you can add other tracks and share your visualization with others.