Converting U-Tube (LabView) data to Fast5¶

Rationale¶

Ideally we want a single file format for both the in-house UTube and MinION devices that are used in the CD lab.

The U-Tube uses LabView for data acquistion and stores measurements as .dat files while the ONT MinION stores the data in .fast5 files.

As the MinION is multi-channeled, stores a lot of metadata, and supports storing events and reads on .fast5 files. The .dat files used of the U-Tube only allow for the storage a single channel of raw data in addition to some metadata.

Instead of creating a third format into which we convert both, it is more sensible to use the .fast5 format as a universal format thanks to its many features.

Method¶

To do so, we need to convert the .dat files into .fast5 files. Both formats quantized the current/voltage signal $y_k$ to some integer $k$ stored in the file.

For the U-Tube, the conversion for signal from stored integers $k$ is as follows:

\[ y_k = (c_0 + c_1 k+c_2x^2) \cdot \frac{1000}{\alpha \beta} \]

with parameters $c_0, c_1, c_2, \alpha \beta$ stored in the metadata of the .dat file. Note that parameter $c_2$ is always assumed to be zero, so this conversion can be simplified to the linear conversion:

$$ y_k = (c_0 + c_1 k) \cdot \frac{1000}{\alpha \beta} $$ The ONT devices also have a similar linear conversion between the stored integers to the signal, but with different parameters:

$$ y_k = (\textrm{offset} + k) \cdot \frac{\textrm{range}}{\textrm{digitalization}} $$ Like in the U-Tube, these parameters are stored in the metadata to allow for conversion of the files data to the measured signal. This means that we can store the same integer values $k` of the .dat file onto the .fast5 file, as long as we include the correct parameters for conversion, which we can algebraically derive as:

\[ \textrm{offset} = \frac{c_0}{c_1}, \;\; \textrm{range} = 1000c_1, \;\; \textrm{digitalization} = \alpha \beta \]