Why the strange high siRNA count in this specific Loci?

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Deng Shun

maybe the sequences of siRNA was highly enriched by its inherent abundance in your RNA-seq database, trying to re-adjust the parameters in your screening threshold.

Jacob O Peter

sounds Good. But I think adjusting the threshold might just eliminate that enriched area. I’m thinking there might be away for me to ID what protein that siRNA targets?

ok, can you check the raw data file, and directly matching the siRNA sequences with the database, if not, maybe the results were not solid

Good idea. I will try this.

Petra Disterer

Jacob,

I'm not clear on what exactly you are doing... that said, if you have the sequence of the siRNA a simple BLASTn search https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch should tell you to what it binds...