TraCeR on 10X cellranegr vdj output filtered_contig.fasta demultiplexed files

[arutik]

Hi,

Similar to this issue Teichlab/bracer#21 (comment) in BraCeR, can one run TraCeR on the per-cell fasta files demultiplexed from filtered_contig.fasta output of cellranger vdj?
If yes, then with what adjustments?

Thank you.

[mstubb]

Yes, I think that should enable you to get the files through TraCeR (although I've not tried it). Is there a reason you want to do that rather than using the Cell Ranger annotations?

[arutik]

Thank you!

I first wanted to do this for BraCeR because I find BraCeR output data more comprehensive (for example, cellranger vdj doesn't output Ig isotype distribution or I can't find it) so I assumed the same would apply to TraCeR vs cellranger vdj, but I guess here there should be no major difference... or is there any TraCeR-specific output?

[mstubb]

I'm not sure it's going to be worth it. The main addition that tracer has is the clonotype graphs but those become too resource-intensive to draw once you get beyond a few hundred cells so I don't think you'll gain much. All the best, Mike

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On 15 Oct 2019, at 16:22, Anna Arutyunyan ***@***.***> wrote: Thank you! I first wanted to do this for BraCeR because I find BraCeR output data more comprehensive (for example, cellranger vdj doesn't output IG isotype distribution or I can't find it) so I assumed the same would apply to TraCeR vs cellranger vdj, but I guess here there should be no major difference... or is there any TraCeR-specific output? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#95?email_source=notifications&email_token=AAIXBBUVTMLIYNSU6B5ALZLQOXN2FA5CNFSM4JA5426KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBJFOGI#issuecomment-542267161>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIXBBWMTD7QKBVBHLMIUT3QOXN2FANCNFSM4JA5426A>.

[arutik]

Thanks a lot! This helps.

Sincerely,
Anna Arutyunyan

[arutik]

Hi,

Coming back to the previous discussion, do you know if cellranger vdj reports CDR3 region sequences like TraCeR and BraCeR do?

Thank you.

Sincerely,
Anna Arutyunyan

[mstubb]

Hi Anna, Yes, the CDR3 sequences are in the Cell Ranger annotation file outputs (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/output/annotation). Note that these are the genuine CDR3 sequences. Tracer reports the ‘junction’ sequences as reported by IgBlast. These are _not_ the canonical CDR3s. So, Cell Ranger’s output is probably more useful. Cheers, Mike

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On 20 Oct 2019, at 13:52, Anna Arutyunyan ***@***.***> wrote:  Hi, Coming back to the previous discussion, do you know if cellranger vdj reports CDR3 region sequences like TraCeR and BraCeR do? Thank you. Sincerely, Anna Arutyunyan — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[arutik]

Thank you very much Mike!

Sincerely,
Anna Arutyunyan

[korakusa]

Hi,
I also would like to run TraCer with 10x genomics data (filtered_contig.fasta output of cellranger vdj) because I'm so interested in TraCer clonotype network graph.
I referred to Teichlab/bracer#21 and split my fasta file.
But in TraCer, there is no --assembled_file option.
How could I run tracer assemble with my fasta files? Should I submit them as a single-end sequencing?

Sincerely,
Sakurako