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alexdobin / STAR

RNA-seq aligner
MIT License
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Quantifying guide RNA (gRNA) using STARsolo #1309

Open papuuk opened 3 years ago

papuuk commented 3 years ago

I am wondering if it is possible to use an index built from just fasta files containing the gRNAs used in single cell pooled CRISPR screen. I can quantify gene counts using STARsolo. But if I try to use the star index built from gRNA and other custom sequences, STARsolo expects a gtf file with genomic loci which I don't have. Is there any way to bypass it in STARsolo?

alexdobin commented 3 years ago

Hi @papuuk

I think there is some good discussion about a similar approach here: https://github.com/alexdobin/STAR/issues/1238

You would need to create an artificial GTF file for your gRNA sequences. It does not need genomic loci, each gRNA sequence is a separate chromosome, and the exon covers its entire length.

Cheers Alex