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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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Output from fasta submission #32

Open NicolasHipp opened 5 years ago

NicolasHipp commented 5 years ago

Hi everyone,

I tested bracer on my single cell rna seq data. I used two approaches: -used both paired fastq from 1 cell The problem with this approach is that bracer recognize multiple BCR_recombinants, so It do not perform all the downstream analyses. When I looked for the TPM of these 2 BCR_recombinant, I have one major BCR and a minor BCR (I assumed that the major clone is the right one).

-used fasta file of BCR generated with BASIC aligner Bracer give me the same clone as the major represented one in the first approach, but when I looked in the output, I don't have the clonotype_sizes.pdf and clonotype_sizes.txt output

Is-it normal if I don't have these both outputs?

I'm also running BALDR on this dataset to confirm that the major clone is the good one.

Ps : Happy new year, thanks for this soft

idalind commented 5 years ago

Hi @NicolasHipp , Happy new year and thanks for the feedback! Did you run bracer summarise for just the one cell you tested, or for multiple cells?