"Valid Barcodes" and "Reads Mapped to Genome"

alexdobin / STAR

RNA-seq aligner

MIT License

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"Valid Barcodes" and "Reads Mapped to Genome" #1878

Open onmyojiyys opened 1 year ago

onmyojiyys commented 1 year ago

May I ask why the value of "Reads Mapped to Genome" is higher than "Valid Barcodes" when I provided a whitelist of barcodes for analysis using STARsolo software? How to use STARsolo to ensure that the reads used for mapping are based on 'Valid Barcodes'?

alexdobin commented 1 year ago

Read mapping is independent of matching barcodes to the passlist. It seems you have a lot of reads with barcodes that cannot be matched. The % of Q30 (high quality) bases look low, which may indicate poor sequencing quality.