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Published 20 hours ago • verified publisher icon liulab-dfci

What is the definition of assemble in the report.tsv?

Open weizhiting opened this issue 3 years ago • 2 comments

Hi, I just a bit confuse about what exactly an assemble in the report.tsv means? I can understand that an assemble in the report file have multiple records, and those records share the same v, d, j region. But I am confuse about why records that share the same v, d, j does not necessary means that they are the come from the same assemble. For example, image those records share the same VDJC but come from different assembles? Thanks for your reply~

weizhiting avatar Sep 02 '21 02:09 weizhiting

The underlying V, J sequence could be quite different due to SHM or the CDR3 sequences. So even if assemble168 has the same V, J, C genes as other assemblies, the assembly is different and gets separated out.

mourisl avatar Sep 02 '21 03:09 mourisl

In the Landscape of B cell immunity and related immune evasion in human cancers, SHMs were defined as mismatches in B cell clusters. So, from report.tsv, How can I get CDR3s from a cluster? Does the CDR3s have the same assemble id (cid column) means that they come from the same cluster?

weizhiting avatar Sep 14 '21 03:09 weizhiting