Closed liboxun closed 1 year ago
You can now download these databases here: https://guidescan.com/downloads
The indices will be added soon. I hope this is helpful!
Perfect. Thanks so much for your prompt response!
@schmidt73 To clarify, the predefined tags cs = specificity score, and ds = cutting efficiency score?
Thanks!
Hi! I was pointed towards here through the ENCODE preprint "Multi-center integrated analysis of non-coding CRISPR screens".
I'm interested in the hg38 and mm10 BAM guide databases, as described in the supplementary method section 3, "Design of sgRNA libraries targeting all ENCODE SCREEN cCREs":
The reason is that I have some promoter-distal genomic regions that I'd like to design gRNAs against, yet ~10% of them are located in places where there are alternative chromosomal segments for. As a result the Guidescan2 webtool doesn't work (finds 0 guide).
The databases described above in the preprint seem precisely the workaround. Would it be possible to share them somehow?
I'd also recommend replacing the guidescan2 webtool's hg38 and mm10 databases with these since I can hardly think of any use cases where users want to design against a fasta that contains alt chromosomes.
Thanks very much!