Can you find the correct transcript in scRNA seq data
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Merav • 0
@429d1874
Last seen 12 days ago
Israel

I have some scRNA seq data, and I want to check and see which transcripts for a specific gene (it has about 5 alternative transcripts) are expressed in a specific cell type. Is that possible?

scRNAseq RNAseq • 128 views
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ATpoint ★ 4.1k
@atpoint-13662
Last seen 3 hours ago
Germany

This is not related to Bioconductor. Generally, biostars.org is a good place to ask. In brief, scRNA-seq is commonly analysed on gene and not transcript level since counts per gene are already low, and even lower for transcripts, plus in end-tagged data ambiguity of reads is often high between transcript per gene. Common preprocessing tools return gene level, so you would need to tweak things.

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