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Is it able to detect large segment deletion in 10X Genome scRNAseq data? #16

Open idibaps001 opened 1 week ago

idibaps001 commented 1 week ago

Hello

Thank you very much for your great work! I run scAllele and got a vcf output. My cells are geneA exon5 knock out cells by CRISPR. But scAllele did not find any deletion in exon5 of geneA.

Would you like to fix this problem?

Thank you very much.

giovanniquinones commented 1 week ago

How long was the deletion? scAllele is limited to micro-indels (no longer than 20 bases)

idibaps001 commented 6 days ago

How long was the deletion? scAllele is limited to micro-indels (no longer than 20 bases)

The deletion is more than 200 bases. I did not find softwares to detect larger-indels for scRNAseq data.

giovanniquinones commented 6 days ago

Was the whole exon removed or only 200 bases of it? If only 200 bases of the exon were removed, what are the length of the flanking regions? You might still be able to find it as a novel splicing event.