Human cell atlas TCR analysis

Question

[datanerd]

HI guys,

Has anyone worked on the human cell atlas TCR data (using h5ad data). How do you extract the TCR form the h5ad datafile for downstream analysis- especially Immunarch or any other tools if anyone has worked on it.

I downloaded the data but couldn't find any information in the meta data after converting it to Seurat object.

Thanks, Mamta

HCA #TCR

Answer 1

[theHumanBorch]

It will likely depend on the data set of interest - I have used several human cell atlas data sets that have sequenced TCR data and the sequences were not included in the .h5ad data. I had to download the individual fastq files and align them.

[datanerd]

Thanks! Seems like that is the case. I couldn't find any of the clonotype info in the meta data.