Running ONT isolate QC

# login to unix environment in powershell (in windows)
wsl

# activate conda environment
conda activate cpgih_utility

Make sure that your data is on the DESKTOP in a folder labelled your RUN NAME.

In this folder, you will have a folder called ‘fastq_pass’, in which there will be folders named after the barcodes eg. ‘barcode01’, in which your fastq.gz files will reside.

Edit the RENAMING.TSV FILE (saved to share_file_templates directory on the desktop) to have the list of all the samples to be analysed (one per line)

The format is barcode## TAB samplename MAKE SURE THE SEPARATOR IS A TAB - example:

barcode25	Sample01
barcode26	Sample02
barcode27	Sample03

Edit the NAMES FILE (saved to share_file_templates directory on the desktop) to have the list of all the samples to be analysed (one per line, with no spaces) - example:

Sample01
Sample02

Run the following:

ont_seq [RUN_NAME]

#eg. 
ont_seq ONT_test