What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA library)

Question

[Swimming bird]

I'm using the human GeCKO Library v2 from Feng Zhang Lab Plasmids (http://www.addgene.org/pooled-library/zhang-human-gecko-v2/) but the gene symbols are outdated (the library was published in 2015). To update them I tried to use this web tool http://www.genenames.org/tools/multi-symbol-checker/ but some gene symbols were not identified.

Is there a better way to update them?

[Ram]

I think you should contact the creators/authors. It's their tool and they're responsible for keeping it up to date. If it's not being maintained, maybe look for alternatives?

[Swimming bird]

The problem is that the CRISPR experiment I'm analysing was already performed with this library... I'll try to contact the creators but I don't expect any answer.

Answer 1

[ATpoint]

You can map back the gRNA sequences to the genome annotation you are using and then intersect the matches with any reference annotation file (GTF) you want. I would use bowtie for this setting gap and mismatch penalty parameters to high values to ensure getting only perfect matches. In the end it is only the sequence that matters, the Cas9 does not care how we call or label whatever sequence in the genome it binds to based on the guide.

[Swimming bird]

Ok, I'll try it. Yes, I know CRISPR/Cas9 does not care about the gene symbols but I want to update them in order to perform a pathway enrichment analysis.