I made use of some of the packages for the analysis of the RNA-Seq data starting from the alignment till the expression analysis. This was just for some of the samples from my large datasets, however, when applying these packages to my large datasets it would be tedious and time consuming, and moreover requires monitoring at the each steps to proceed with the next. For this purpose, I would like to write a batch script to run the analysis for my set of samples. To begin with writing a script or pipeline, it would be nice if you can share some methods and materials that could be helpful for me.
QC checks Adapter trimming STAR Aligner QC checks Quantification Expression analysis
Thank you, Toufiq