de.STAIR RNA-Seq scripts

Place for some of our scripts.

For an introduction to git you might want to explore a Github tutorial

Feel free to contribute, fork or add! For editing mark down, please see cheat sheet

Source code

R code written and executed in RStudio (R version 3.4.3)

Python code written in Spyder3 (Python version 3.6)

Unix stuff executed with (Ubuntu 16)

de.STAIR

See project details at de.STAIR project page

Tools

• Demultiplexing flexbar
• Quality check with good old fastqc or qualimap
• Pre-processing fastx - alternatively trimmomatic or trimgalore
• Mapping kallisto
  • See for reference genomes: RefSeq or Ensembl
• DE Analysis and statistics with kallisto sub-sequent tool sleuth
  • Preferred setup for larger data sets, because kallisto is incredibly fast
  • Sleuth needs R/Rstudio
  • Alternatively using traditional mappers like Star or Hisat2
  • TRAPLINE only for showcases =P