Is the donor id information published for the TCR sequencing data? It does not appear to be in the contig_annotations csv. Thank you!
Created by sierra7 Thank you very much Marina! I appreciate all of your help with this. Yes, the technology includes measuring gene expression, surface protein, TCR, and BCR from the same cells.
Kind regards,
Marina Amazing! Thank you so much for explaining this. I really appreciate it.
Just one more question?from what I read in the supplemental information of your paper, it seemed like although the donors were the same for the TCR and scRNA-seq data, the cells were barcoded differently. Just to clarify, you are saying that they are?in fact?the exact same cells sequenced on both the overall scRNA-seq and the TCR sequencing data? all_pbmcs.tar.gz is data after demultiplexing and all the quality check steps, so part of the cells were filtered out. Meanwhile, TCR files in the folder are raw, after alignment. So, researchers might use it if they decide to reanalyze the gene expression data (for example change the filtering steps, etc). That is why you see more cells in the TCR files or inside fastqs rather than in the all_pbmcs.csv. As for cell types, they were assessed by the gene expression data and surface protein information. For TCR we took only the information that was overlapped for cells that were annotated as T cells.
Kind regards,
Marina Hi Marina!
Thank you for your quick reply.
I have been using the csv file from all_pbmcs.tar.gz. However, the reason I did not think I was using the correct metadata is because not all the cell ids from the TCR sequencing are mapping to cells in all_pbmcs.tar.gz metadata csv file. Also, some cell ids from the TCR sequencing data say they are mapping to cell types other than just T cells. I had assumed this was because the cells used for the TCR sequencing data are not the same as the scRNA-seq data, so the metadata for both could not be the same.
However, I then found this was also the case when I tried to map all the cell ids from the fastqs scRNA-sequencing data to this all_pbmcs csv. Not all cells from these scRNA-seq fastq files mapped to the metadata.
Are you instead saying to use the individual cell type files under GEX_HTO_processed and ignore this all_pbmcs one?
Thank you again.
Best,
Sierra Hello @sierra7,
All the metadata for TCR is matched with metadata for GEX data, as the technology provides simultaneous profiling of the V(D)J repertoire and gene expression (GEX) data.
Please refer to the GEX gzipped data for T cells (folder GEX_HTO_processed). Within this gzipped data, you will find a file named metadata.csv. You can integrate TCR and GEX by using the cell barcode id and file name.
Kind regards,
Marina