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MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
MIT License
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Obtain transcript count matrics #110

Open hejian41 opened 2 months ago

hejian41 commented 2 months ago

Hi Shuangshuang,

Considering a gene can produce multiple transcripts, is there a method to obtain a transcript counting matrix instead of a gene-based one during data preprocessing?

Thank you!

lishuangshuang0616 commented 2 months ago

Single-cell RNA sequencing captures mRNA fragments from the polyA tail at the 3' end, making it challenging to recover longer sequences that can provide information about the originating transcript. To accurately quantify transcripts, methods like single-cell full-length capture or Smart-seq, which offer full-length coverage, may be required.

hejian41 commented 2 months ago

Got it. Thanks for your reply.

lishuangshuang0616 commented 2 months ago

I'm not sure the BRIE2 can fulfill your need, https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02461-5

hejian41 commented 2 months ago

Apologies for the delayed response. BRIE2 identify gene differentiation through spliced and unspliced states, not transcript variants. My objective is to assess gene targeting efficiency, given elements inserted into a specific gene transcript. Thank you for suggestion.