visualizing target region on exons

[Andreas Jung]

Hi folks,
my goal is to project the target regions of my amplicons in the exons of the genes. When using IGV' s region tool the target region is projcted onto the genome but cuts off eventually part of an exonic structure Thus I do not see, how much is missing. Is there a way to visualize selected exons of a gene together with the region and in case the target region is located in intronic parts of the genes these too. In other words the area of the genome containing the minimum and maximum genomic part spanned by exon and target region.

Thank you ver yn much for your help and support. Have a great and successful dqya nd best luck with your work.

Andy

[Helga Thorvaldsdottir]

Hi Andreas,

I'm not sure what you are referring to by the "region tool". I guess you mean either (a) you are importing your target regions into IGV and viewing them with Regions>Region Navigator, or (b) you created a list of your target regions and are viewing them using Regions>Gene List ? Either way, IGV cannot automatically extend the regions based on nearby exons. I assume you have a large number of target regions and that you don't want to extend them by hand in IGV. To create a list of extended regions before you import them into IGV, try using bedtools (http://bedtools.readthedocs.io/en/latest/) to compute the overlap between your target regions and the gene exons.

Helga

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