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BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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What is IGHDM subtype? #52

Open SabrinaITNL opened 4 years ago

SabrinaITNL commented 4 years ago

Hi, quick question: the IGHDM subtype indicates that both the IGHM and IGHD constant chain were mapped for that particular reconstructed BCR? So the cell contains the reconstructed heavy chain "attached" to the IGHM and IGHD constant chain?

Many thanks! BW Sabrina

SabrinaITNL commented 3 years ago

Hi, just to follow up on this request. In the "IMGT_gapped_db" output from Bracer summarize, the field ISOTYPE and the field C_GENE are not always identical (as I would expect from the field name). In particular when ISOTYPE == "None" , the C_GENE == "IGHDM". In the "changeodb" output you then have the fields ISOTYPE and C_CALL. In this case the two fields are identical, so for ISOTYPE == IGHDM, also C_CALL == IGHDM. Now my question remain: what does this "IGHDM" isotype stand for? And why in the "IMGT_gapped_db" it is actually given as ISOTYPE=="None".

We are in the process of submitting data were we used Bracer and we need this clarification asap, so any reply is greatly appreciated.

Many thanks Sabrina

idalind commented 3 years ago

Hi Sabrina, The IGHDM isotype indicates that the same reconstructed sequence was found in combination with the IGHM and IGHD constant regions. When it comes to differences in C_call and isotype, this likely is the result of many identical reconstructed sequences being collapsed in each cells, some of which include the C_region while others don't. If you send me the bracer assemble result directories for a couple of cells with this issue I can give a more detailed explanation as to what has happened.

Best regards, Ida (ida.lindeman@medisin.uio.no)