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TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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TraCeR on 10X cellranegr vdj output filtered_contig.fasta demultiplexed files #95

Open arutik opened 4 years ago

arutik commented 4 years ago

Hi,

Similar to this issue https://github.com/Teichlab/bracer/issues/21#issuecomment-417711510 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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

On 15 Oct 2019, at 16:22, Anna Arutyunyan notifications@github.com 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?

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arutik commented 4 years ago

Thanks a lot! This helps.

Sincerely, Anna Arutyunyan

arutik commented 4 years ago

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 commented 4 years ago

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

On 20 Oct 2019, at 13:52, Anna Arutyunyan notifications@github.com 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 commented 4 years ago

Thank you very much Mike!

Sincerely, Anna Arutyunyan

korakusa commented 4 years ago

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