Hello!

I have a question about analysis of sncRNA. I have used WIND previously and now we are using SPORTS1.1, to match a previously published analysis. The output of SPORTS is the sequence and some (poor) annotation and count data. With the count data we were able to get the statistically significant sncRNA using standard methods, but now I have a set of sequences with very little annotation, mainly RNACentral identifiers. So I can get some Ensembl IDs, using biomaRt, but many don't exist for these sncRNA sequences.

I need to correlate the binding site(s) to some gene function. I have been using miRanda3.3 which will work with any sequence that is input, but I feel like I am not doing something important.

The sequences are short from ~20nt to 150nt and the Phred scores are all max. I have the alignment bam files with the multimappers and I was thinking about how ChiP-seq peaks can be localized to genes.

Any ideas or guidance would be greatly appreciated

Thank you