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Difference between assembledCells.clns vs contigs.clns? #64
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Hi,
TheassembledCells.clnsfile 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.clnsfile, on the other hand, contains clonotypes generated before grouping.
I ran the
analyze 10x-sc-5gexpreset and I would like to run thefindAllelesafter 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?