Error in repLoad, unsupported format

[mengfeiwangdmu]

Hello,

I am trying to analysis TCR data from a published article named"Pan-cancer single cell landscape of tumor-infiltrating T cells". But I failed in the input data, I used repLoad, it showed: unsupported format. The file is 10X VDJ.txt format. And I checked the file, compareing with other 10X VDJ .CSV files, it missed three columns named "contig_id", "raw_clonotype_id" and "raw_consensus_id". I don't know if it is possible to input the file without these three colums, and how to do it. If it's impossible, I will ask the author for the source data.

Hope for your reply.Thank you.

Best regards, Mengfei Wang Dalian Medical University

[Alexander230]

Hello, Mengfei! I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

You can add these columns to your file, filled with None values; for example, using sed (change my_10x_file.csv to your file name here):

sed -i '1s/$/,contig_id,raw_clonotype_id,raw_consensus_id/; 2,$s/$/,None,None,None/' my_10x_file.csv

If you have more questions, feel free to ask them!

Best regards, Aleksandr