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lmdu / krait

An ultrafast tool for genome-wide survey of microsatellites and primer design
http://krait.biosv.com
GNU Affero General Public License v3.0
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Mapping SSR #20

Open ArzooShamoon opened 3 years ago

ArzooShamoon commented 3 years ago

One of the Reviewers raised a query "distribution of identified SSRs in different genomic regions". I tried to run on both Linux and Windows operating systems. Identification of SSRs and their statistical report was perfectly obtained but while analyzing annotation files no results were obtained. I downloaded the GFF, GTF, and GFF3 files from NCBI and Ensemble. Please guide me regarding this issue.  Thanking you Screenshot (30) Screenshot (31)

lmdu commented 3 years ago

You can check the sequence name is the same or not in your annotation file and sequence file.

ArzooShamoon commented 3 years ago

Respected sir In this case we cannot examine location of identified SSRs in other genomes? Like if i identify SSRs in Grevillea robusta we cannot search the distribution of these identified SSRs in Eucalyptus annotation file?

On Wed, May 19, 2021, 1:48 PM Lianming Du @.***> wrote:

You can check the sequence name is the same or not in your annotation file and sequence file.

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lmdu commented 3 years ago

Yes, the mapping function in our program is just comparing the coordinates of SSRs with gene features not alignment to locate SSRs to genes.