Running PURC

After running the fluidigm2purc script, you will have a new directory named output-FASTA. The next in the process is to run PURC. We will do this for each FASTA file individually using a Bash for loop. The script from PURC that we will run is called purc_recluster.py. Make sure that it is in the main PURC folder and also that it is in your PATH. The code below is an example of what this would look like if you are running things on a Unix-flavored computer.

cd output-FASTA/

# Loop through all of the fasta files and run purc_recluster.py
for f in *.fasta
do
    purc_recluster.py -f $f -o output-PURC \
                      -c 0.975 0.99 0.995 0.997 -s 2 5 --clean
done

We have also included a modified version of the purc_recluster.py script as part of our pipeline (purc_recluster2.py). The only difference is that it conducts fewer iterations of the chimera detection and clustering steps. If you would like to use it, make sure that move or copy it from the Fluidigm2PURC folder into the main PURC folder. Also, it also only requires two clustering thresholds for the -c option.