at which stage can i select the confidence threshold?

[ArashDepp]

• 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?