Identification of piRNA/siRNAs from small RNA-seq data

Question

[jkkbuddika]

Hi,

I am in the process of analyzing a collection of small RNA datasets from flies (Drosophila melanogaster). So far this is what I have done:

1. Trim adaptors using cutadapt and extract 18-30nt long sequences.
2. Align to the Drosophila genome using Bowtie (not Bowtie2): Reads with at least one alignment 80-85%
3. Count miRNAs using featureCounts using miRBase annotations.
4. I also use ShortStack to identify potential novel small RNAs.

Now I want to identify piRNAs and siRNAs from my data. I see there are a couple of piRNA databases with piRNA data (like piRNAdb and piRBase). Can I use a GTF from one of these databases to identify piRNAs? How about siRNAs?

Thanks,

KB

[Gjain]

An important point here is to make sure you do not loose reads with multi mapping as many piRNAs are similar sequences.