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QC I: Intro
The purpose of this exercise is to introduce you to common tools to asses the quality of sequencing data and filter it according.
Your task is to run different tools for quality control (FastQC, FastQ Screen and multiQC) and filtering (FASTX Toolkit, Trim Galore! and PRINSEQ) of sequencing data .
Write a report where you shortly describe the differences/advantages/drawbacks of the different tools. Justify your preference towards any of the tools.
Answers to marked questions with a 'Q', are for you to explore different output files, you do not need to include them in the report.
Our data involves sequencing data from different sequencing applications:
- http://onlinelibrary.wiley.com/doi/10.1002/mgg3.115/full
- https://www.encodeproject.org/: ENCFF121FBT, ENCFF931PQC, ENCFF836ILC, ENCFF263KEN, ENCFF831GJV, ENCFF017GWO
- http://www.ebi.ac.uk/ena: ERR1523947, ERR1523948, ERR1523949
- Other data courtesy of JBP and CJ
Connect to the server using MobaXterm (PC users) or your local Terminal (MACS users):
ssh -X your_account@rudy.biomedicine.gu.se
Set the environment by:
cp /home/teacher3/.bashrc .
source .bashrc
This file contains the paths to some tools you will be using.