number of barcodes 10 fold lower in Star Solo vs CellRanger ARC GEX

[akhst7]

Hi,

I just could not figure this out. I have a dataset from 10x, PBMC from a Healthy Donor - Granulocytes Removed Through Cell Sorting, looking at GEX not ATAC. A barcode created by CR-ARC v1 has 11909 barcodes whereas Start Solo using 10x'5 gets only 1232 barcodes. A following is my Star Solo script;

#!/opt/homebrew/bin/zsh

index=/Volumes/MySlateDrive/star_genome_index/index_human_Gencode_GRCh38_p13
whitelist=/Volumes/MySlateDrive/10X_Whitelist/737K-arc-v1.txt
r1=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
r2=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
r3=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R1_001.fastq.gz
r4=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R2_001.fastq.gz

STAR --genomeDir $index \
--runThreadN 50 \
--readFilesCommand 'gzip -c -d' \
--readFilesIn $r1,$r3 $r2,$r4 \
--soloCBwhitelist $whitelist \
--soloType CB_UMI_Simple \
--soloCBstart 1 \
--soloCBlen 16 \
--soloUMIstart 17 \
--soloUMIlen 12 \
--soloStrand Forward \
--soloBarcodeMate 1 \
--clip5pNbases 58 0 \
--twopassMode Basic \
--soloMultiMappers EM \
--soloFeatures Gene GeneFull \
--outFilterMultimapNmax 1 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--soloCellFilter  EmptyDrops_CR \
--outReadsUnmapped Fastx \
--outFileNamePrefix /Volumes/MySlateDrive/pbmc3Ksorted.reverse \
--outSAMtype None
#--clipAdapterType CellRanger4 \

I set --soloCBlen, --soloUMIlen, and --clip5pNbases according to 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user manual, 16 nt 10x Barcode (for GEX), 12 nt unique molecular identifier (UMI), and a 30 nt poly(dT) sequence are also released. . I also modified the code according to discussions in #1381, and #768. At this point, I'd really appreciate any input on what I am missing.

Thanks.