Hey guys
Bear with me as I am new to the bioinformatics field, but I'm motivated to learn
Currently I am planning to perform single cell BCR sequencing (scBCRseq) and trying to learn the workflow. Normally you would need an HCP and some R programming to run the cell ranger pipeline and interpretation of the data. If this is incorrect, I apologize.
Long story short, 10x released its Genomics Cloud Analysis in Q4 of 2021(https://www.10xgenomics.com/products/cloud-analysis) and it seems simple compared to the alternative methods. I believe you can upload the sequenced fastqs and custom references to the cloud account (in browser or command line) and then it will execute cell ranger pipeline. It will then provide output files(.vloupe) that you can view in Loupe to visualize.
I am just looking for just clonotypes and vdj sequences. Is that the workflow or am I missing some steps? Do I need to anything to the fastqs beforehand after single cell sequencing? Can I get all the data I need in that output file, and will loupe provide that visualization?
New to this so any advice or explanation will be super helpful. Thank you!
