Hello,
I am interested in using the nf-core/oncoanalyser pipeline for homologous recombination deficiency (HRD) analysis. I have a couple of questions regarding the compatibility and usage of the pipeline with specific data:
Compatibility with IonTorrent BAM Files: Is it possible to use nf-core/oncoanalyser to analyze BAM files generated by the IonTorrent platform? If so, are there any specific considerations or adjustments that need to be made when importing these files into the pipeline?
Using the Oncomine Comprehensive Assay Plus (Thermo Fisher): I would like to know if it's feasible to use nf-core/oncoanalyser for HRD analysis with data from the Oncomine Comprehensive Assay Plus panel by Thermo Fisher. Although the documentation mentions support for the TSO500 panel, I am curious whether a similar analysis can be performed with the Oncomine Comprehensive Assay Plus panel, and what modifications might be necessary.
Thank you for your assistance.
Best regards
It might be best to ask this question in their github repository.
Thank you for the suggestion! I've already posted the question on the GitHub repository, but I haven't received a response yet. That's why I'm also seeking help here, hoping that someone who has worked with this pipeline or encountered the same issue might be able to assist. Any advice or shared experiences would be greatly appreciated. Thanks again!
Whilst we try to be responsive in nf-core, waiting for 1 day for a response on an open source project is not unusual ;) Especially one that had it's first release only this week and has developers based in Australia.
nf-core has a Slack community which is where most community members communicate, there is a dedicated channel for each pipeline (including
#oncoanalyser) so that's your best bet for getting a response. You can find a link to join here: https://nf-co.re/joinLink to GitHub issue for future viewers of this thread: https://github.com/nf-core/oncoanalyser/issues/92
Thank you : )