Step-by-step bioinformatics analysis of schistosoma mansoni long non-coding RNA sequences

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In the last few years, long non-coding RNAs (lncRNAs) have been widely studied in humans, and their relevance for physiological and pathological conditions has been demonstrated. In parasites, there are only a few works, such as in Plasmodium falciparum, where it was shown that an lncRNA regulates the expression of a gene associated with immune system evasion, also indicating the relevance of understanding the role of this class of RNAs in parasites. In Schistosoma mansoni, in the last 2 years, there were four published articles related to the annotation of lncRNAs in different life cycle stages using RNA-Seq libraries. In order to make this process of lncRNA identification and annotation more accessible to biologists with no bioinformatics training, considering the growing number of S. mansoni RNA-Seq libraries publicly available from different sources, such as ovary tissues from bi-sex and single-sex infections, and the potential of lncRNAs as therapeutic targets, we provide this step-by-step protocol of lncRNA identification and quantification. This guide includes the download of RNA-Seq libraries from a public database and reads processing and mapping against the genome, transcript reconstruction, novel lncRNA identification, transcripts expression level determination, and the identification of differentially expressed lncRNAs.
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