scirpy.read_10x_vdj(path, filtered=True)

[taopeng1100]

Hi I like to read multiple "filtered_contig_annotations.csv" files from 10x; how can I do this in scirpy.read_10x_vdj?

Thx,

Tao

[grst]

Hi Tao,

you can read them in a loop and concatenate them.
It works the same way as for adata files without TCR information, see the solution here:
scverse/scanpy#267

Hope that helps and let me know if you have further problems!

Best,
Gregor

[taopeng1100]

Thx! I will try it. From: Gregor Sturm <notifications@github.com> Sent: Wednesday, April 22, 2020 1:56 PM To: icbi-lab/scirpy <scirpy@noreply.github.com> Cc: Peng, Tao <tpeng@fredhutch.org>; Author <author@noreply.github.com> Subject: Re: [icbi-lab/scirpy] scirpy.read_10x_vdj(path, filtered=True) (#121) Hi Tao, you can read them in a loop and concatenate them. It works the same way as for adata files without TCR information, see the solution here: scverse/scanpy#267<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_theislab_scanpy_issues_267&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=MUCsUp7fpukHcLu3vEbp-p33bAWRdJifyZuHm8qCO4E&s=ySi0brF_hl4gYU01uNUxIlcxp1sfTotYwHBJaCSm0jE&e=> Hope that helps and let me know if you have further problems! Best, Gregor — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_icbi-2Dlab_scirpy_issues_121-23issuecomment-2D618035721&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=MUCsUp7fpukHcLu3vEbp-p33bAWRdJifyZuHm8qCO4E&s=21QYJESdErjxqJAY2HZgIW7hxdKXA9RIN25xhWas1rk&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALCZ3CKIOQB2HLE3EX5VN7DRN5KVPANCNFSM4MOOJQFQ&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=j6EgtEBZ-6pbDONgnwVzuTHJ6L-gWcikckOhZCwVjPc&m=MUCsUp7fpukHcLu3vEbp-p33bAWRdJifyZuHm8qCO4E&s=y19f7-0T-bozH84fIXjMrLyg8yG0G-MF1Ni4R392zRg&e=>.

[JLTrincado]

Dear authors,

I'm using the solution proposed here for loading multiple 10x vdj files. For some reason, after concatenating some cells loses information. Here I load 2 files and concatenate them. Prior to concatenation, the shown cell has TRA_1_cdr3 region. After concatenating, the region has disappeared. This only happens with some cells, not all. What am I missing?

Thanks for your help.
Juan L.

[grst]

Hi Juan,

could it be just the order of columns?
The concatenation seems to sort columns alphabetically, s.t. the TRB_1_cdr3 column is hidden in the middle (...) or the pandas data frame.

Best,
Gregor

[JLTrincado]

Hi again,

thanks for the quick reply. It wasn't because of the order in the columns, but thanks to that I realize it was my bad when calculating the TCR neighbors. I was using receptor_arms="all" instead of "any". That's why this cell didn't show up as clone.

Thanks again and congratulations for your work.
Best.

[grst]

@taopeng1100, I will close this now. Let me know if you have further issues.