RepLoad 10X data about immunarch

[margaretc-ho]

I have the same question! I am following these instructions https://immunarch.com/articles/web_only/load_10x.html#prepare-10x-data and trying to read in the data downloaded from this 10X genomics dataset (seems like a very standard dataset) and the filtered_contig_annotations has the following columns:
barcode is_cell contig_id high_confidence length chain v_gene d_gene j_gene c_gene full_length productive cdr3 cdr3_nt reads umis raw_clonotype_id raw_consensus_id donor origin
and not the following columns that RepLoad is looking for. Namely I get the error:

> file_path = "/Users/homc/Library/CloudStorage/TEST_BCellFlu_data"
> immdata_10x <- repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Processing "/Users/homc/Library/CloudStorage/TEST_BCellFlu_data" ...
  -- [1/5] Parsing "/Users/homc/Library/CloudStorage/TEST_BCellFlu_data/sc5p_v2_hs_B_flu_aggregated_5gex_b_vdj_b_clonotypes.csv" -- unsupported format, skipping
  -- [2/5] Parsing "/Users/homc/Library/CloudStorage/TEST_BCellFlu_data/sc5p_v2_hs_B_flu_aggregated_5gex_b_vdj_b_consensus_annotations.csv" -- 10x (consensus)
  -- [3/5] Parsing "/Users/homc/Library/CloudStorage/TEST_BCellFlu_data/sc5p_v2_hs_B_flu_aggregated_5gex_b_vdj_b_filtered_contig_annotations.csv" -- 10x (filt.contigs)
Error in `df[, vec_names]`:
! Can't subset columns that don't exist.
✖ Columns `cdr1_nt`, `cdr1`, `cdr2_nt`, `cdr2`, `fwr1_nt`, etc. don't exist.
Backtrace:
 1. immunarch::repLoad(file_path)
 2. immunarch (local) .process_batch(batches[[batch_i]], .mode, .coding)
 3. immunarch (local) .read_repertoire(.filepath, .mode, .coding, ...)
 4. immunarch (local) parse_fun(.path, .mode, ...)
 5. immunarch:::parse_repertoire(...)
 9. tibble:::`[.tbl_df`(df, , vec_names)

Any suggestions? @vadimnazarov

[margaretc-ho]

It seems like this is a common issue that many others are having when trying to load in 10X Genomics data
#363
#358
We are all seeming to get this same error because of the column names
So far, seems no solution