dandelion on bulk data about dandelion HOT 3 CLOSED

Hi Sara, if you can generate/convert the bulk data to the AIRR format with the default required rearrangment schema in the .tsv file, Dandelion should be able to read it with ddl.Dandelion('file.tsv'). It will use the sequence_id as the cell_id which should then work for all down stream purposes.

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Thanks Kelvin.
Then what input data I should use to generate the filtered_contig_dandelion.tsv file?
Can you provide more details about the steps? Sorry, I am not so clear about what steps I need to do.

Thanks,
Sara

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It depends on what the manufacturer of your BCR-seq library kit reccomends. Off the top of my head, you would have to either use presto or MiXCR and then export as AIRR format if your data is in fastq format. Usually your library kit provider will tell you directly what you should use, as they come with custom primers information which you will need to provide into those softwares anyway.

If your data is already in fasta format, you can i) run MiXCR in shotgun mode, ii) use igblastn, iii) use IMGT/High V-QUEST(https://www.imgt.org/IMGTindex/IMGTHighV-QUEST.php) and obtain the AIRR files.

As this sounds like it is outside the immediate scope of dandelion as it doesn't handle those bits above, your questions would probably be better placed directed at the developer of those other softwares.

Any more help/information about this would require substantially more involvement from me, and would require a formal e-mail to my supervisor (Professor Menna Clatworthy [email protected]] to request a collaboration.

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