Finding common small RNAs between two FASTQ datasets.

Question

[bteefy8]

Hi All,

I'm fairly new to bioinformatics so please forgive me if this question is a bit pedestrian.

I'm trying to assign expression of particular miRNAs to certain cell lineages within my poorly characterized model organism. The datasets that I have are

1) immunoprecipated small RNAs from the entire organism

2) lineage-specific small RNA libraries.

Both of these small RNA datasets are in FASTQ format. I was wondering if there is a way that I can query each of the lineage -specific small RNA libraries against my miRNA library to find which miRNAs are expressed in each lineage. The end goal would be to generate lists of indexed miRNA sequences present in each of the cell lineages.

Any help is greatly appreciated.

Thank you.

[WouterDeCoster]

within my poorly characterized model organism

Does this mean you don't have a reference genome available?

[bteefy8]

I'm told it is an incomplete assembly, but yes, a reference genome is available.