naive question about tracer

[GuidoLeoni]

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]

Hi Guido, Are you thinking of doing this on bulk or single-cell rnaseq from tumour tissue? Thanks, Mike

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On 20 Jun 2018, at 06:38, GuidoLeoni ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#69>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABFwhpTX0n_ByKhTD2UczBfbZhnA9JLYks5t-lBkgaJpZM4UvSro>.

[GuidoLeoni]

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

[mstubb]

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

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On 20 Jun 2018, at 09:01, GuidoLeoni ***@***.***> wrote: bulk rnaseq from tumor tissue (CT26 mice) sequenced with 60mln of PE reads — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#69 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABFwhiup82fGCXyy98W1phakfevjjl6Pks5t-nHmgaJpZM4UvSro>.