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# System prepended metadata

title: Revision session - Day 2

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# Revision session - Day 2

## Feedback

* The pace seem to be fine, but keep on informing us :slightly_smiling_face: 
* The introduction to nextflow seemed to raise interest while still a bit confusing to some. If there is time and interest, we will run the actual pipeline you looked at in your group today. 
* The instructions for the nextflow group exercise felt "vague" to some of you. This is, to be perfectly frank, by design :sweat_smile:. The rationale is to expose you to a "real-life" situation, with just a minimal amount of help/guidance for you to follow through. So that when faced with such a situation in the future, you will be used to navigate it with- out/limited - guidance. 

## Any Questions?

## Assessment #1
1. In which way has second generation sequencing been a game changer?

	Faster (much! 2.4 billion PE reads in 44 hours on an Illumina NovaSeq S4), less labour intensive, which drove the cost down below 1000$ for sequencing a human genome at a 20X coverage.

2. Third generation sequencing methods are better because of their increased sequencing depth - TRUE or **FALSE**?

3. Why is ribosomal RNA filtering important?
    
    ```To remove noncoding RNAs and enrich for mRNAs which reflect gene expression```
    
    ```Normally, we extract the total RNA of cells (samples) and ribossomal RNA (rRNA) is about 80% of total RNA, which is not translated into proteins. If we are interesting in sequencing the messenger RNA (mRNA-seq) we should remove rRNA.```
    
4. List the steps in the data preprocessing pipeline

	QC -> (rRNA sorting) -> QC -> (quality / adapter trimming) -> QC -> (pseudo-)alignment -> Biological QA

5. The ribosomal RNA filtering and the adapter and quality based trimming are mandatory steps in the pipeline. I.e. They need to be run no matter what. - TRUE or **FALSE**?

