NanoporeSeqBasecalling

For the deep learning course project.

We are going to build a model that will translate the electronic signals by Nanopore signals to DNA sequence.

To Start

First install gcloud SDK Clone the project and attempt to run uploadAndRun.sh

Try to run the script or just copy past it into terminal/cmd. The script will upload the keras folder to my gcloud VM instance, run the execute the model locally, and then download the output locally.

Note that you may want to update the following two lines based on your operation system

rm -rf keras\output
mkdir keras\output

For windows use \ as path sepator, for MAXOS and linux, use / as path separtor

Input preprocessing

We start from the sample from keras example from gcloud ml-samples

Extract and update the input preprocessing module

The sample input is placed at data folder

As of 10/26/2017, We are able to extract information from both .signal and .label file and run the simple feedforward network on them.