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Title: | Long non-coding RNAs annotation in Strongylocentrotus purpuratus. Studying the need of a reference genome. |
Author: | Doblado Martín, Sonia |
Tutor: | Pegueroles Queralt, Cinta |
Others: | Maceira, Marc |
Abstract: | The aim of our project is to investigate the feasibility of annotating lncRNAs without a reference genome. In order to estimate the accuracy of the annotations, we selected a species (Strongylocentrotus purpuratus) having both a reference genome and RNA-Seq data publicly available. First, we obtained a transcriptome de novo assembly, using the software Trinity. We then used two approaches to annotate lncRNAs via FEELnc: i) we obtained a list of putative lncRNAs by filtering the de novo transcripts using several criteria and ii) we used a machine learning method fed with already annotated lncRNAs. Finally, we compared the results from both methods between them and also to the lncRNAs set obtained mapping directly to a reference genome, which is the standard protocol. According to our results, it would be possible to annotate the lncRNAs without a reference genome. There's a difference in the amount of annotated lncRNAs between our two sets of only 1,03%, and we have found 41,6% of the lncRNAs annotated using a reference genome in the most recent paper available for S. purpuratus. |
Keywords: | transcriptome lncRNA de novo assembly |
Document type: | info:eu-repo/semantics/masterThesis |
Issue Date: | Jan-2021 |
Publication license: | http://creativecommons.org/licenses/by-nc-nd/3.0/es/ |
Appears in Collections: | Trabajos finales de carrera, trabajos de investigación, etc. |
Files in This Item:
File | Description | Size | Format | |
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Long non-coding RNAs annotation in Strongylocentrotus purpuratus. Studying the need of a reference genome..mp4 | 24,43 MB | MP4 | View/Open | |
Diapositivas Long non-coding RNAs annotation in Strongylocentrotus purpuratus. Studying the need of a reference genome.pdf | 1,11 MB | Adobe PDF | View/Open | |
sdobladomTFM0121memoria.pdf | Memoria del TFM | 1,31 MB | Adobe PDF | View/Open |
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