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.
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