CellBender can not remove the backgroud very well using the output of STARsolo

[JianhuaWang95]

Hello, I'm running CellBender using the output of STARsolo, however, I found that CellBender can not remove the backgroud very well. Only no more than 50 cells been removed. However, when I run CellBender using the output of CellRanger, the results are much better.

Here is the commond I used to run STARsolo:

STAR --genomeDir /pmglocal/ \ --runThreadN 10 --soloType CB_UMI_Simple --soloCBwhitelist /pmglocal/3M-february-2018.txt \ --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 \ --readFilesIn /pmglocal/sample1_S1_L001_R2_001.fastq.gz,/pmglocal/sample1-seq2_S1_L001_R2_001.fastq.gz \ --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outSAMmultNmax 1 \ /pmglocal/sample1_S1_L001_R1_001.fastq.gz,/pmglocal/sample1-seq2_S1_L001_R1_001.fastq.gz \ --readFilesCommand zcat --soloBarcodeReadLength 0 \ --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx \ --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM \ --outTmpDir /pmglocal/tmp/sample1/ --outStd Log \ --clipAdapterType CellRanger4 --outFilterScoreMin 30 \ --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR \ --soloUMIdedup 1MM_CR --soloCellFilter EmptyDrops_CR --soloOutFileNames sample1/ features.tsv barcodes.tsv matrix.mtx \ --outFileNamePrefix sample1/ --soloFeatures Gene GeneFull Velocyto SJ

Here is the commond I used to run CellBender:

cellbender remove-background --input /pmglocal/sample1/GeneFull/raw/ --output /pmglocal/sample1/GeneFull/raw/cellbender.h5 --cuda --epochs 75

The version of CellBender is 7.2.0.

Is there any suggestion?

Thanks!