zktuong/dandelion

dandelion on bulk data

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saramoein372 commented

Description of the question

Hi Kelvin,

I have a question about how to run the dandelion on bulk data? Cell ranger output are only generated on single cell.
But dandelion needs filtered_contig_annotation.csv and filtered_contig.fasta.

Would you please help me to solve this issue, when I can not run cell ranger on my data?

Thanks,
Sara

Minimal example

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zktuong commented

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.

saramoein372 commented

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

zktuong commented

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 mrc38@medschl.cam.ac.uk] to request a collaboration.