Open bengarcia015 opened 9 months ago
Hi Ben, for BCR analysis we need to have nucleotide data, but it seems like you don't have one in the IMGT data. Is this correct?
Is there a way to export IMGT files in AIRR Standard Format instead of the format that IMGT uses?
I have imported both formats, including the IMGT-exported AIRR formatted data, and it seems like that may have solved some of the issues. However, I am still running into one main error when loading the data:
[!] Warning: found NAs in clonal counts. Setting them to 1's.
I think the error may initially have been caused by my use of PRESTO as the pre-IMGT cleaning method, which collapses down the counts and puts that into the name. I have removed them from the name, and put them into the AIRR formatted document in the "consensus_count" column, is there another column where I should put these counts so that they can be loaded into the "clones" entry of the immunarch object?
🐛 Bug
I am currently trying to analyze BCR sequencing data by using IMGT HiV-QUEST data before using immunarch for further analysis. I should note that I am analyzing BCR data from Rainbow Trout (Oncorhynchus mykiss) and attempting to use the BCR pipeline, so I am not sure if this is causing any of the issues I am encountering. This is my first time reporting a bug, so I apologize if there is too much/not enough information, or if there is anything I missed here! Overall, the package is working beautifully, except for a couple of issues:
First, when using repLoad on the .airr files that were exported from IMGT, I receive a number of errors, copied below. The airr file is directly downloaded from IMGT, with no modifications:
The organization of the O. mykiss VDJ loci is different to that of mammals, so it is certainly possible that this is causing some of the issues with the "not logical" values being reported.
The next issue I have encountered arises with repGermline. The code and outcome are listed below:
I have tried going through and modifying the names to remove the "Oncmyk_Sw " and "Oncmyk_Sw" from the names, as well as everything except for the core portion of the locus name, to no avail.
Thank you for any help you are able to offer, and please let me know if there is any further information/data that you need to help diagnose this!
Ben