piRNA seq

Question

[daffodil]

Hi, PiRNA seq data can be mapped to transcriptome assembly to identify piRNA precursors. Is there a reason why we have to map to the transcriptome? Best

[biofalconch]

Hopefully the model system you are using contains RNA samples from when piRNA are being transcribed. They are polyA and capped transcripts so in principle piRNA precursors should be in the transcriptome. For me wouldn't take this as a given and map to the genome rather than the transcriptome and you can use tools like featureCounts to see if they really come from transcripts, or ShortStack to find these clusters (found here).