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Human cell atlas TCR analysis

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

tcr cell single
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written by datanerd datanerd

1 answer

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.

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written by theHumanBorch • theHumanBorch

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

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written by datanerd datanerd

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