How to plot Inactivating mutations in TOGA2

[fishman311]

I recently updated to TOGA2 and noticed that the result file "inactivating_mutations.tsv" is different from the "inact_mut_data.txt" file of TOGA. How can I draw the plot for "Inactivating mutations"? Thank you.

[ReverendCasy]

Hello @fishman311 ,
One easy way way is to extract the projection SVG from BigBed file stored in the ucsc_browser_files directory:

bigBedToBed ucsc_browser_files/${your_prefix}.bb stdout  | awk -F’\t’ “($4 == your_transcript_of_interest){print $31}"

For more complicated cases, like combining SVGs for multiple transcripts from multiple runs, you can use the Rust script at src/rust/target/release/combine_plots (available in v2.0.6). The script is not yet fully tested, and the proper user interface will be likely added to the upcoming TOGA2/Postoga release.

Plotting projections absent from the final TOGA2 input (and, by proxy, the BigBed file) is not currently possible but we can add the respective code to the upcoming TOGA2 release if there’s demand for the feature.

[fishman311]

Hello @ReverendCasy,

Thank you for the quick and very helpful response! The method of extracting SVG strings directly from the BigBed file is exactly what I was looking for.

I have a follow-up question regarding the files in the ucsc_browser_files directory (such as the .bb and .ix files):

What is the recommended way to visualize these files collectively? Should I upload them to a web server and use the "Custom Tracks" feature on the UCSC Genome Browser by providing the URLs, or is there a way to view them locally (e.g., using IGV or a specific TOGA2 utility)?

I would appreciate any tips on the best workflow for browsing these results in a genomic context.

[ReverendCasy]

Hi @fishman311 ,
Thank you for asking, for we’re actually missing the UCSC code in the T2 repo. General strategy does not differ from that for original TOGA (see here for the UCSC plugin code and the tips on track description). You might also want to upload the decorator track (${prefix}.decorator.bb) to the browser to visualise inactivating mutations right in the browser view.

We have not yet tested using the same files with IGV or any other genome browser but I guess it must be feasible.