Hi Everyone, I am new to using the nf-airrflow pipeline, and have a question that I can't seem to find the answer to. I am waiting for the sequencing data to come back from an experiment, where I have used the Takara Bio SMART-BCR with UMI kit to perform bulk BCR (IgH) analysis on. Looking at the usage documentation, I think I need to use the 5' RACE as the library generation method, and therefore supply the c-primers and Linker sequences in fasta format. Unfortunately these are not available in either the documentation or if you email tamara (they are proprietary). Whats the best way to use the pipline if these details are not available?

Hi James this is indeed tough to do with airrflow and immcantation if you dont have the primers. I think Gisela mentions some ways with which one might be able to extract the primers somewhere here (maybe even to me 😅 ) but I dont know too much on how this is possible. We are however currently working on a way to introduce mixcr into airrfow which is a tool which doesnt need the information as the algorithm works a little differently. You could try to run airrflow with mixcr from this pr https://github.com/nf-core/airrflow/pull/346. There you can also check the updated docs on how to do it but essentially you can set a flag and mention your libary and (I think

--preset takara-human-rna-bcr-umi-smartseq

). Then you run the sequence assembly step with mixcr and all postprocessing with airrflow, so the output doesnt change for you (except for when you also want some of the mixcr postprocessing=

Thanks - I'll try the mixcr pr. I have used mixcr for BCR analysis, and was hopeful to use airrflow as it seems to be a comprehensive analysis pipeline.

great. If you run into any troubles, please let me know

Hi @James O'Brien, sorry for the very late comment as I’m on maternity leave at the moment and have limited time to reply. Airrflow 4.2.0 already supports directly the Takara protocols, and it is made easier so that the users do not need to provide the primers. There are two Takara protocols that I know of, the SMARTer and SMARTseq. Which one did you use?