Writing a batch script for analyzing RNA-Seq data

Question

[mohammedtoufiq91]

Hi,

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.

Workflow type:

QC checks
Adapter trimming
STAR Aligner
QC checks
Quantification
Expression analysis 

Thank you, Toufiq

Answer 1

[WouterDeCoster]

What you are looking for is a workflow manager such as Snakemake or Nextflow (and others). This workflow might do what you need, or require minimal adaptations: snakemake RNA-seq workflow using STAR and DESeq2

[mohammedtoufiq91]

Thank you. This was helpful.