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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:
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
However, what I need is a more detailed result. Can Starsolo achieve this, or which parameters do I need to adjust?
![image](https://private-user-images.githubusercontent.com/58845320/398360935-75623073-0f05-4b36-8262-c5c35c249f65.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.eI-DT69bBoSqfFkGrq6BPnWv7MUE7fxWChHizwATVK8)
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