Open papuuk opened 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
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?