No matching of cell barcode from umi_count/ with GEX cells barcode

[liuyang2006]

Dear author,

I use CITE-seq-Count successfully got the results with mapping rate > 95%. But when I overlap cell barcode with my GEX gene expression data, there is no overlapping.

Even I convert barcode with "-1" suffix.

Here is my command:

CITE-seq-Count \
    -R1 $indir/$r1 \
    -R2 $indir/$r2 \
    -t /project2/sli68423_1316/users/yang/u01/data/TAG_LIST.csv \
    -cbf 1 -cbl 16 -umif 17 -umil 26 -cells 10000 --start-trim 10 \
    -o citeseq_out_${tagname}

Here is the CITE-seq-Count output barcode:

zcat barcodes.tsv.gz | head
TCATGCCGTGCTACAT
GTCGTTCGTCAACGAG
AGATCGTCACCACACG
TGTTACTTCGCCTTCG

Here is the GEX data barcode:

zcat barcodes.tsv.gz | head
AAACCCAAGCCTCACG-1
AAACCCAAGCCTGACC-1
AAACCCAAGTATTGCC-1
AAACCCAAGTCGAATA-1
AAACCCACACGCTGCA-1

Do you have any suggestions to figure out the problem?

Thank you