DeepTE analysis Project (see paper)
Fall 2023: Classifying Transposons using DeepTE. A multi-CNN model. My team of four including myself enjoyed analyzing the paper results, we utilized publicly available transposons from the Zenodo library and its metadata to extract the TEs of C-Elegans and O-Sativa. We then exported the data to multiple CSV files and fasta files for preprocessing and selection for partial training and testing DeepTE. My main contribution was through writing many scripts, python and SBatch to run DeepTE classification on the O-Sativa transposons as well as on the data file provided by the author. We had regular meetings throughout the semester and put together dynamic plans that we often revisited to compare classification results on O-Sativa versus the author-provided data. We created a presentation to demonstrate our findings.
