Difference between assembledCells.clns vs contigs.clns?

[pursellta]

I ran the analyze 10x-sc-5gex preset and I would like to run the findAlleles after but am unsure if I should be using the assembledCells.clns or the contigs.clns file for this? I have looked and can't seem to find any documentation about the difference between these files.

Could you provide information on the differences between them and which you recommend using for the findAlleles and export clones steps?

[mizraelson]

Hi,
The assembledCells.clns file contains chains grouped by cells. If you want to reconstruct paired-chain single-cell SHM trees later, this is the file you should use.

The contigs.clns file, on the other hand, contains clonotypes generated before grouping.