Mapping SSR

[ArzooShamoon]

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

[lmdu]

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

[ArzooShamoon]

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?

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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. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#20 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUD56FU43JZOK4TSKAAJL4LTONX3TANCNFSM45C3BWVA> .

[lmdu]

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