Navoda Wijesuriya

Thank you for reaching out about this genomics analysis challenge. Assessing copy number variation of SSR loci through read mapping is an excellent technique. Let me offer some guidance based on best practices:

First, align your sample reads against a reference genome using a tool like BWA-MEM. This creates a BAM file mapping each read. Then use software like SAMtools to identify reads mapping to your target SSR coordinates.

The read depth or coverage at an SSR locus indicates copy number. A consistent depth close to the genome-wide average implies a single copy locus. Significantly higher coverage suggests multiple copies. You can statistically compare depth distributions to identify outliers.

There are robust tools like CNVnator that can automate and streamline the analysis process for you. But manually inspecting alignments in a genome browser is also insightful for small-scale assessment.

Feel free to reach out if you need help interpreting results or finding suitable software. Optimizing these bioinformatic techniques does involve some initial learning. But you are pursuing a very fruitful approach to characterize your SSRs.

Thank you very much