search

satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
Other
2.31k stars 920 forks source link

Demultiplex VDJ data #3873

Closed amufaamo closed 3 years ago

amufaamo commented 3 years ago

Hi, I have scTCR fastq and hashtag fastq of 10x Genomics. We don't have scRNA-seq fastq. Can we demultiplex scTCR data?

k3yavi commented 3 years ago

Hi @amufaamo ,

Thanks for reaching out. Unfortunately, it's not clear to me what kind of demultiplexing you are talking about ? Is it like the experiment based HTO hashes or you are talking about fastq demultiplexing ? If the former I think you can use the HTODemux command to demux the experiment.

yuhanH commented 3 years ago

You can align your HTO fastq feature-barcode by Cellranger or Alevin. Then you can use HTODemux or follow our cell hashing vignette to demultiplex your cells.

amufaamo commented 3 years ago

Sorry my question was not so clear.

If I have scRNA-seq + scVDJ-seq + hashtag feature barcode fastqs, I can demultiplex scRNA-seq and scVDJ-seq into samples. But I have only scVDJ-seq + hashtag feature barcode fastqs. So can I demultiplex scVDJ-seq fastq?

2021年1月9日(土) 3:06 Yuhan Hao notifications@github.com:

You can align your HTO fastq feature-barcode by Cellranger or Alevin https://combine-lab.github.io/alevin-tutorial/2020/alevin-features/. Then you can use HTODemux or follow our cell hashing vignette https://satijalab.org/seurat/v3.2/hashing_vignette.html to demultiplex your cells.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/satijalab/seurat/issues/3873#issuecomment-756912856, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK5RGCYZ2JC3NKSUXW67FBLSY5CSNANCNFSM4VMAEKOQ .

yuhanH commented 3 years ago

If the cell barcodes are the same, you can demultiplex your scVDJ-seq

amufaamo commented 3 years ago

Thank you so much. I will try it.

2021年1月12日(火) 22:59 Yuhan Hao notifications@github.com:

If the cell barcodes are the same, you can demultiplex your scVDJ-seq

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/satijalab/seurat/issues/3873#issuecomment-758672639, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK5RGC5AHFLFHSYHJ45DKXLSZRIVPANCNFSM4VMAEKOQ .

csweeney225 commented 3 years ago

I am trying to do the same thing but am also unable to find a way of demultiplexing my V(D)J data with Seurat. I have 10X Chromium data (5' gene expression, V(D)J and hashtag for multiplexing). I can see the vignette for how to demultiplex the gene expression data, which all makes sense.

How do I demultiplex the V(D)J data? What V(D)J output file from Cell Ranger should I use?