Scripts in this repository can be used to reproduce all results in manuscript "Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts".
The script preprocessing.sh was used for data pre-processing.
Scripts for analysis were organized in folders based on the datasets they were applied to. For each folder, the .R script was used for the actual analysis.
In total 5 datasets were analyzed, including
-
The Zymo native synthesized oligo nanopore sequencing dataset (./zymo/) [1].
-
Thymidine analogs-containing primer extension dataset (./nmeth/primer_extension/) [2]
-
Native yeast genomic DNA nanopore sequencing datasets (./nmeth/yeast/) [2]
-
NA12878 cell line mRNA dataset (./mrna/) [3].
-
E.coli 16S rRNA nanopore sequencing dataset [4], containing the following 3 sub-datasets. Please note the event tables were provided by the authors of the original study, therefore data pre-processing is not applicable here.
5a. Native strain (./rrna/native_ecoli_16s_rRNA/).
5b. Pseudouridine-deficient (Psi516) strain (./rrna/Psi516_deficient_ecoli_16s_rRNA/).
5c. m7G-deficient (m7G) strain (./rrna/m7G_deficient_ecoli_16s_rRNA/).
References:
- Rand, A. C., Jain, M., Eizenga, J. M., Musselman-Brown, A., Olsen, H. E., Akeson, M., & Paten, B. (2017). Mapping DNA methylation with high-throughput nanopore sequencing. Nature methods, 14(4), 411.
- Mueller, C. A., Boemo, M. A., Spingardi, P., Kessler, B. M., Kriaucionis, S., Simpson, J. T., & Nieduszynski, C. A. (2019). Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nature methods, 16(5), 429.
- Workman, R. E., Tang, A. D., Tang, P. S., Jain, M., Tyson, J. R., Razaghi, R., ... & Sadowski, N. (2019). Nanopore native RNA sequencing of a human poly (A) transcriptome. Nature methods, 16(12), 1297-1305.
- Smith, A. M., Jain, M., Mulroney, L., Garalde, D. R., & Akeson, M. (2019). Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PloS one, 14(5), e0216709.