Week 1: Welcome!

Meeting Notes

All slides presented are in week_1_slides.pdf.

Teams

Neural Network Implementation

• Raw DNA to Tensors, What are our options?
• One Hot encoding (2D)
• What layers make sense to include?
• Incorporate more data (mapped TFBS, DNAseI, species relatedness, ect)

Quality Control Pipeline

• Quantify and analyze the input data
• Are these sequences valid?
• Which sequences do we remove?
• Visualize

TFBS mapping

• Map all TFBS onto sequence
• Visualize TFBS and conservation
• Make tools for community

To do for next week

• Email your team preference
• Give me your github username
• In the folder fasta_exercise. Make a program that reads in the pdm2_neurogenic.fa and performs one or all of the tasks mentioned below. You can perform in R or Python. When you have a working script, please up load into the fasta_exercise directory. Please fork repo and make pull request to add.

Program Tasks:

• Make a sequence alignment
• turns sequences into a basic python / R data structure
• measures GC content per sequence