I want to examine the presence of Quelling mechanism ( in fungal genomes of interest) that is related with the suppression of transposons expansion in eurkayotic genomes. Since, Quelling pathway is associated with the production of small interfering RNAs that guide RISC complex to fascilitate transcriptional and post-transcriptional silecing of homologous RNAs (mRNAs). I think this approach will assist me in confirming the presence of Quelling in the fungal genomes I am studying.
I would suggest to use CLC genomics work bench (QIAGEN) and install GOseq as a plugin. You can build a pipeline between CLC and GoSeq. Good luck.
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-genomics-workbench/
There are several commercial software which can be used however, not everyone has access to those software and their paid services. Therefore, I don't think it's a good idea to recommend such commercial software.
Please take a look at these open-source/open-access pipelines which can be effectively used for the analysis of siRNAs:
1) Pogorelcnik R, Vaury C, Pouchin P, Jensen S, Brasset E. sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data. Mob DNA. 2018;9:25. Published 2018 Jul 31. doi:10.1186/s13100-018-0130-7
2) Sivarajan Karunanithi, Martin Simon, Marcel H. Schulz. Automated analysis of small RNA datasets with RAPID. bioRxiv 303750; doi: https://doi.org/10.1101/303750 Now published in PeerJ doi: 10.7717/peerj.6710
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