I’m using bracer to process my single cell data but I found that the assembled contigs are not so similar to the IMGT reference according to the result of Igblast.
For example, when I used Tracer to porcess the data, the similarity (identity(%) by Igblast) between the assembled contigs and the IMGT V/J reference are almost more than 99%, like the example below.
When I used Bracer, the similarity seemed to be very low, often less than 95%，even less than 90% in some samples, like the examples below.
As a result , most of （more than 90%） T cells or Macrophages in my data also had a positive result（bearing BCR） according to the bracer output.
So I‘m wondering if the “synthetic BCR genomes” was designed well enough to extract BCR-derived reads. It seems that many false positive reads were included, effecting the down stream analysis results.
I’m using bracer to process my single cell data but I found that the assembled contigs are not so similar to the IMGT reference according to the result of Igblast.
For example, when I used Tracer to porcess the data, the similarity (identity(%) by Igblast) between the assembled contigs and the IMGT V/J reference are almost more than 99%, like the example below.
When I used Bracer, the similarity seemed to be very low, often less than 95%，even less than 90% in some samples, like the examples below.
As a result , most of （more than 90%） T cells or Macrophages in my data also had a positive result（bearing BCR） according to the bracer output.
So I‘m wondering if the “synthetic BCR genomes” was designed well enough to extract BCR-derived reads. It seems that many false positive reads were included, effecting the down stream analysis results.