search

liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data
MIT License
274 stars 47 forks source link

Does TRUST4 work with whole exome sequence (WES) data? #175

Open WangKang-Leo opened 1 year ago

WangKang-Leo commented 1 year ago

Hello,

Do you think TRUST4 can work with whole exome sequence (WES) data? Perhaps, it could provide more information if it runs for both normal blood and normal samples. If not, do you know any other tools could do that?

Thanks in advance

mourisl commented 1 year ago

It does (as mentioned here #102). But I haven't got a chance to explore the sensitivity and check potential biases from the primers in WES.

WangKang-Leo commented 1 year ago

It does (as mentioned here #102). But I haven't got a chance to explore the sensitivity and check potential biases from the primers in WES.

I am sorry to ask the same question again. I am working with a multi-omics cohort, where the treatment response is regarded as endpoint. Our RNA-seq data have potential batch effect issues, and I found that output metrics from TRUST4 are not associated with our endpoint. But when I run this tool (https://github.com/McGranahanLab/TcellExTRECT) using our WES data, which showed expected correlation (higher T cell fraction, more likely respond) and are consistent with our other results. So I am afraid that I have to run TRUST4 using WES data. Can I do that?

mourisl commented 1 year ago

Yes, you can. The command is the same.