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maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
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Whether the input sequence can be mRNA sequence when gff3 file is given for a new species genome? #43

Closed tiramisutes closed 1 year ago

tiramisutes commented 4 years ago

Hi, I have cloned this software locally and want to run for a new species genome. I want to know whether the mRNA sequence not each exon sequence for an mRNA can input when provided a gff annotation file? Thanks.

maximilianh commented 4 years ago

In many cases, this would mean extremely long input sequences... but yes, if you remove/increase the input sequence limit you can input all exons.

You cannot input the mRNA. CRISPR is a genome-editing tool. It cannot modify the places in the mRNA that go over splice junctions.

On Fri, May 1, 2020 at 3:09 AM hope notifications@github.com wrote:

Hi, I have cloned this software locally and want to run for a new species genome. I want to know whether the mRNA sequence not each exon sequence for an mRNA can input when provided a gff annotation file? Thanks.

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tiramisutes commented 4 years ago

So I'm little troubled by it. All exons are mean mRNA (from start to stop codons, for example full length CDS of AT3G47570.1). If we cannot input the mRNA sequence, what is the purpose of gff3 file that input when adding a genome use crisprAddGenome command?

maximilianh commented 1 year ago

The purpose of the GFF file is so you can see where the off-targets are. Users care a lot about to know if an off-target is in a gene or not.

In theory the GFF could be used to pick guides, given a transcript or gene. But I'm not there yet. Maybe in 2-5 years... :-)