using python to run bioinformatics pipeline
Please, how to use python to run bioinformatics pipeline (Pipeline used by Li et al., 2014):
1) Importing fatsq files
2) Quality Data filtering
3) Tim the data with poor quality
4) Mapping against Reference: hisat2
5) Gene level counts (Quantification)
6) Differential Expression Analysis
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What do you mean? Please provide much more detail, as your question isn't really usefully answerable at the moment.
What pipeline? What data? What is the actual question about running the workflow - is it a problem with a particular program?
The purpose of biostars is to help you, but not to do your work for you. This question shows zero effort in solving this yourself.