This quick start document will walk through what to do when running Herald for the first time.
Experiments
Experiments are equivalent to a MinKNOW experiment; i.e. where you record the information prior to sequencing.
Herald uses MinKNOW experiments to group samples.
Create an experiment
To create an experiment, first click on the create experiment
button to access the submission form and then fill in the following fields:
Experiment name
This is the unique name to give this experiment. All data for this experiment (including any samples you create later) will be kept in a directory with this name.
note: your value for
experiment name
can contain spaces but these will be replaced with underscores in all file names that are derived from this value.
Output location
This is where you want the experiment data to be stored.
Once you have entered both Experiment name
and Output location
and have clicked onto the next box, the form will autocomplete to indicate where the data will be stored.
example: if you entered
my experiment
and/Users/myname/data
, the form will autocomplete yourFAST5 data
directory to/Users/myname/data/my_experiment/fast5_pass
The app will also check the proposed directories - if fast5_pass
or fastq_pass
is found, the app will assume you are entering details for an existing experiment and will tag the sample as sequenced and basecalled already.
Fill in any other details and then click on the create sample
button on the bottom of the form
A success message should appear and the number of available experiments will have increased in the app dashboard.
Samples
Processes
Once an experiment or sample has been tagged with a process, it can't be removed. The process will be marked as complete when it has finished.
note: If an existing experiment has been added (which already has fast5 or fastq data), the sequence
and basecall
tags will be added but marked to complete
straight away.