scRNAseq - infer type of single-cell chemistry from fastq
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3 months ago
predeus ★ 1.6k

Hello all,

it's a known thing there's lots of variants of single cell experiments - e.g. kb --list from kallisto-bustools lists at least 10 different variants. If you're processing a reasonably big selection of scRNA-seq experiments, it would make sense to try and infer it automatically.

Is there by any chance a tool that can guess the chemistry from the reads?

Thank you in advance, as always.

scRNA-seq single cell RNA-Seq • 158 views
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Perhaps the only thing possible with 10x data (assuming sequencing recommendations were followed strictly) is to look at the length of reads and check.

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Thank you. 10x is easier, yes - although 5' is still tricky.