tumor pair pipline question

[Michele Tinti]

Hi, I'm considering starting to use gene pipe, in particular, the tumour pair analysis to study differences in wild-type and mutated strains of human pathogens. 

Do you think is feasible to run the tumour pair pipeline on sequences different from humans?

thanks for your attention!

Michele

[José Héctor Gálvez]

Hello Michele, 

While it is indeed possible to use the pipeline for the application you describe, it is not the intended use, so there will be several adjustments and tests required before it works seamlessly. We would only recommend that kind of use for advanced users who are familiar with the ini system and are able to generate their own reference genomes with the required indices to run the pipeline.  If this is your first time using the tumor-pair pipeline, it might be hard to adapt it right away. 

However, from a theoretical perspective, yes the use that you are suggesting is possible with this pipeline. My suggestion is to first run the regular DNA-seq pipeline (which is the "base" pipeline that tumor-pair is forked from) and see if the variant calls you obtain are promising. If your results with DNA-seq are good, you can explore ways to adapt tumor-pair to do the work that you are looking for. Does that make sense?

I hope this answers your question. Let me know if you need any clarifications or additional advice. 

Best,

Jose Hector Galvez

Bioinformatics Specialist

Canadian Centre for Computational Genomics

Office Tel. (514) 746-8812

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