Parameters for running pipeline with ArcherDx data

[wudustan]

I have some RNA Seq fusion panel data generated with ArcherDx

Description of feature

I provide some ArcherDx fusion pipeline data here: https://drive.google.com/file/d/1Ly7WZEo732qBSobsLOVdBpzJVRRCotOn/view?usp=sharing

The specific sequencing panel is FusionPlex Pan Solid Tumor v2 18091 v1.1

Would it be possible to have some guidance on how to change the rnafusion parameters to work with this data?

It's expected for this sample to have an MN1 - PATZ1 fusion

[brianjohnhaas]

It looks like there's some adapters on these reads that would need to get trimmed off. I expect this could be impacting the fusion calling by STAR-Fusion.

Here's an example screenshot for the MN1 region from the STAR aligned bam file and you can see the mismatches at the very 5' end.

After doing some form of read trimming, you could give STAR-Fusion another try.

I did run these data through FusionInspector with just MN1--PATZ1 as the target, and it did find one nice read supporting this fusion. Usually we hope for more reads. It might be that both FusionInspector and STAR-Fusion will do better once the reads are cleaned up.

[rannick]

Adding the label as no changes will be made to the code, leaving open for discussions

[wudustan]

Thanks. I've been busy with other projects but will be addressing this shortly. It's going to be a bit of a reverse engineering job. I have the output files from the internal ArcherDx pipeline so I need to figure out how the adapters are processed.

[rannick]

I will close this for now, but it would be interesting to hear your reporting with this if you have had any success, feel free to reopen if needed