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sambamba flagstat issues in STARsolo #2260

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onmyojiyys opened this issue Dec 24, 2024 · 0 comments
Open

sambamba flagstat issues in STARsolo #2260

onmyojiyys opened this issue Dec 24, 2024 · 0 comments

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@onmyojiyys
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When I used Starsolo to align single-cell transcriptome data, the generated BAM files seemed to be somewhat abnormal. When using the sambamba flagstat command to count, the output results were as follows:

STAR --genomeDir GRCh38/star --readFilesCommand pigz -dc --clipAdapterType CellRanger4 --readFilesIn test.R2.fastq.gz test.R1.fastq.gz --limitGenomeGenerateRAM 100000000000 --limitBAMsortRAM 100000000000 --soloType CB_UMI_Complex --soloCBwhitelist barcode_segment1.xlsbarcode_segment2.xls barcode_segment3.xls --soloBarcodeReadLength 0 --runThreadN 16 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloOutFileNames test --soloCellFilter EmptyDrops_CR 10000 0.99 10 45000 90000 1000 0.01 20000 0.01 10000 --outSAMtype BAM SortedByCoordinate --soloCBmatchWLtype 1MM --soloCBposition 0_0_0_7 0_26_0_33 0_52_0_59 --soloUMIposition 0_60_0_67 --soloUMIlen 8 --outSAMattributes NH CR GX GN CB UB HI AS nM

image

However, what I need is a more detailed result. Can Starsolo achieve this, or which parameters do I need to adjust?
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