Closed kapsakcj closed 4 years ago
Might be good to experiment with this flag with NanoPlot:
--drop_outliers Drop outlier reads with extreme long length.
Either that, or drop the --loglength
flag
After some experimentation, my preferred nanoplot cmd and params is this:
runID=N20169-20-004
NanoPlot -t $NSLOTS --summary sequencing_summary.txt --loglength --N50 --prefix $runID -o nanoplot --maxlength 100000
--drop_outliers
removes too much of the longer reads. It cut out everything above 25kb (different depending on the run, of course)
Add NanoPlot to the gpu-basecalling workflow to run after basecalling finishes below this line: https://github.com/lskatz/nanoporeWorkflow/blob/228abfd6a790c67a5d4a468fafca64b8896876fe/workflows/run_01_basecall-w-gpu.sh#L122
Need to make a new script,
np_runsummary_nanoplot.sh
which includes something like this: