Tracer summarise output

Question

Tracer summarise output

Opened this issue 6 years ago · 3 comments

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 'cell_data.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

Answer 1 · 2018-08-31T10:22:35.000Z

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

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On 27 Aug 2018, at 11:00, YarsnC ***@***.***> 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 'cell_data.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 <#75>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABFwhk8mnBAUyKNIqQQD9uRz3zcBfvG-ks5uU7VAgaJpZM4WNbgW>.

Answer 2 · 2018-09-20T05:52:03.000Z

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

Answer 3 · 2018-09-21T13:12:01.000Z

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

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