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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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naive question about tracer #69

Closed GuidoLeoni closed 6 years ago

GuidoLeoni commented 6 years ago

Thank you for your work with Tracer it is a very great tool Might it be used also for analyzing rnaseq data from a mouse tumor tissue sample? If yes according to your experience can be identified a low confidence limit in the number of reads that contribute to identify a productive TCR? Best Guido

mstubb commented 6 years ago

Hi Guido,

Are you thinking of doing this on bulk or single-cell rnaseq from tumour tissue?

Thanks,

Mike

On 20 Jun 2018, at 06:38, GuidoLeoni notifications@github.com wrote:

Thank you for your work with Tracer it is a very great tool Might it be used also for analyzing rnaseq data from a mouse tumor tissue sample? If yes according to your experience can be identified a low confidence limit in the number of reads that contribute to identify a productive TCR? Best Guido

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GuidoLeoni commented 6 years ago

bulk rnaseq from tumor tissue (CT26 mice) sequenced with 60mln of PE reads

mstubb commented 6 years ago

Hi Guido,

I’m pretty confident that TraCeR would reconstruct something from this sort of data but we didn’t design it for this purpose and haven’t done any testing of its performance or accuracy when used on bulk data. It may well be better to try MiXCR for this:https://mixcr.readthedocs.io/en/master/

Hope that helps.

Very best,

Mike

On 20 Jun 2018, at 09:01, GuidoLeoni notifications@github.com wrote:

bulk rnaseq from tumor tissue (CT26 mice) sequenced with 60mln of PE reads

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