search

Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
Other
123 stars 48 forks source link

Tracer summarise output #75

Open YarsnC opened 6 years ago

YarsnC commented 6 years ago

Hi!

Thanks a lot for this wonderful work!

My colleague did some analysis using tracer and we're a little bit confused about the output file 'celldata.csv' and 'recombinants.txt'. It seems that some cells are not mentioned in these two files. (No 'No seqs found for TCR['A', 'B', 'G', 'D']' message for these cells in recombinants.txt either). According to the filtered_TCRs.txt file of some of these cells I checked, they do have recombinants successfully assembled.

I'm wondering if these cells are filtered somewhere? Did I miss something?

Best,

Dana

mstubb commented 6 years ago

Hi.

Please could you send some examples of outputs that are discordant like this. I can then start to explore what’s going on.

Thanks!

Mike

On 27 Aug 2018, at 11:00, YarsnC notifications@github.com wrote:

Hi!

Thanks a lot for this wonderful work!

My colleague did some analysis using tracer and we're a little bit confused about the output file 'celldata.csv' and 'recombinants.txt'. It seems that some cells are not mentioned in these two files. (No 'No seqs found for TCR['A', 'B', 'G', 'D']' message for these cells in recombinants.txt either). According to the filtered_TCRs.txt file of some of these cells I checked, they do have recombinants successfully assembled.

I'm wondering if these cells are filtered somewhere? Did I miss something?

Best,

Dana

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Teichlab/tracer/issues/75, or mute the thread https://github.com/notifications/unsubscribe-auth/ABFwhk8mnBAUyKNIqQQD9uRz3zcBfvG-ks5uU7VAgaJpZM4WNbgW.

YarsnC commented 5 years ago

P03_A_1266.zip P03_A_1272.zip P03_A_1275.zip P03_A_1295.zip P03_A_1331.zip P03_A_1346.zip P03_A_1355.zip P03_A_1374.zip P03_T_0005.zip P03_T_0008.zip

mstubb commented 5 years ago

Hi,

These cells all look like they might be MAIT cells (they have a TRAJ1-2-to-TRAJ33 alpha chain) and so are filtered out by TraCeR to avoid the appearance of expanded clonotypes that are less likely to be interesting. Please can you check a couple of things:

  1. If you look in TCR_summary.txt you should see these cells reported as potential MAIT cells at the bottom.

  2. If you run summarise with the --keep_invariant option it should now report these cells in cell_data.csv and recombinants.txt.

Let me know if that helps. This is a nice review on MAIT cells (and other unconventional T cells): https://www.nature.com/articles/ni.3298 https://www.nature.com/articles/ni.3298

All the best,

Mike

On 20 Sep 2018, at 06:52, YarsnC notifications@github.com wrote:

P03_A_1266.zip https://github.com/Teichlab/tracer/files/2399840/P03_A_1266.zip P03_A_1272.zip https://github.com/Teichlab/tracer/files/2399841/P03_A_1272.zip P03_A_1275.zip https://github.com/Teichlab/tracer/files/2399842/P03_A_1275.zip P03_A_1295.zip https://github.com/Teichlab/tracer/files/2399843/P03_A_1295.zip P03_A_1331.zip https://github.com/Teichlab/tracer/files/2399844/P03_A_1331.zip P03_A_1346.zip https://github.com/Teichlab/tracer/files/2399845/P03_A_1346.zip P03_A_1355.zip https://github.com/Teichlab/tracer/files/2399846/P03_A_1355.zip P03_A_1374.zip https://github.com/Teichlab/tracer/files/2399847/P03_A_1374.zip P03_T_0005.zip https://github.com/Teichlab/tracer/files/2399848/P03_T_0005.zip P03_T_0008.zip https://github.com/Teichlab/tracer/files/2399849/P03_T_0008.zip — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Teichlab/tracer/issues/75#issuecomment-423048478, or mute the thread https://github.com/notifications/unsubscribe-auth/ABFwhtfnqS5KTNYDvIOizbYRxCMrc2Inks5ucy0DgaJpZM4WNbgW.