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phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
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Merging Multiple TCR Files #46

Closed kkearns13 closed 1 year ago

kkearns13 commented 1 year ago

Hi,

Thank you for developing CoNGA! I have an integrated RDS object and 11 TCR contig files generated from TRUST4 in a 10x format, but I wasn't sure how to compile them into one file so that I could run CoNGA. I looked at issue #28 which referenced a function called make_10x_clones_file_batch but I couldn't find this script? I made a .csv file with two columns for the file path and suffix (-1, -2, etc.). I also saw that there is some documentation for merging multiple datasets https://github.com/phbradley/conga/blob/master/README.md#merging-multiple-datasets-into-a-single-object-for-conga-analysis but am not sure how to amend it to add the suffix to the barcodes etc. Any help would be much appreciated! Thank you!

kkearns13 commented 1 year ago

Oh never mind! I was looking in the wrong place - I didn't realize it wasn't its own script. For future reference you can import it with: from conga.tcrdist.make_10x_clones_file import make_10x_clones_file_batch

phbradley commented 1 year ago

OK, glad you figured it out; and sorry it wasn't more clear to begin with! Take care, Phil

From: Kendall @.> Sent: Monday, July 25, 2022 2:44 PM To: phbradley/conga @.> Cc: Subscribed @.***> Subject: Re: [phbradley/conga] Merging Multiple TCR Files (Issue #46)

Oh never mind! I was looking in the wrong place - I didn't realize it wasn't its own script. For future reference you can import it with: from conga.tcrdist.make_10x_clones_file import make_10x_clones_file_batch

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kkearns13 commented 1 year ago

No worries! I'm not used to python so it's a bit of a learning curve for me!