Question: Locate sgRNA on gene target
gravatar for sd74y28r
4.5 years ago by
sd74y28r0 wrote:

Dear all,

I have a list of sgRNA that were designed for CRISPR experiment and their corresponding gene (symbol).

I'm trying to compute a percent peptide score, that is the location of these guides along their target.

I need to find a way to align all these sequences along their target and output the location of the alignment as well as the size of the gene.

I though about using a shell script along with an alignment tool but I need help in getting it started.

Thank you in advance.

alignment • 1.1k views
ADD COMMENTlink modified 4.5 years ago by ATpoint46k • written 4.5 years ago by sd74y28r0
gravatar for ATpoint
4.5 years ago by
ATpoint46k wrote:

sgRNAs are usually designed to perfectly match the target. I would start by finding out which reference genome has been used and then use the bowtie short read aligner, not allowing any mismatches, outputting only the best alignment. Make a multifasta of all sgRNAs and feed it into bowtie. That should give you the exact targets. From there on, you can simply use the coordinates of the targets and a gene annotation list (e.g. from UCSC) to intersect both targets and genes. Once you know the gene, you can get sizes and everything from the annotation file as well. Hope that helps.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by ATpoint46k
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