at which stage can i select the confidence threshold? #170
Description
- spladder version: 3.0.2
- Python version: 3.7
- Operating System: Linux
Description
I am using the spladder for large cohorts using the workflow described here:
https://spladder.readthedocs.io/en/latest/spladder_cohort.html
The events that i detected were filtered using confidence level 3. I want to decrease the confidence level in order to obtain more number of events. so my question is, at what stage can i make this change.
The steps that I used are listed on https://spladder.readthedocs.io/en/latest/spladder_cohort.html, and include single graph, merged graph, Quantification, and event calling.
Could you please tell at which step can i change the confidence value.
Secondly, in all of the steps, i used parallel option, but despite that, program always ran on a single CPU. for example:
spladder build -o $outputDIR -a $GTF -b listOfBamFiles.txt --merge-strat merge_graphs --no-extract-ase --validate-sg --validate-sg-count 3 --parallel 10
runs a single process, despite the --parallel option being set to 10. It is the case with all the four steps that I used.
Could you please suggest something in these two issues?