# Whole genome bisulfite sequencing data

## Getting to know the pipeline:

#### What pipeline was used?
nf-core/methylseq

#### What was used to build the pipeline?
Nextflow

#### Where can you find information on the pipeline?
https://nf-co.re/methylseq

#### Was the run successful? Where can you find that information?
yes, execution_report.html

#### How long did the run take? Which tool took longest to run?
8h 38s, ~140 core hours
bismark_align (4h 55m 6s)

#### What is the output of the pipeline?
results_description.html

## Getting to know the samples:

#### What do we know about the samples?
2 samples, homo sapiens, non-medicated females with rheumatoid arthritis, samples taken from the knee (synovial membrane) at the Academic Medical Centre (AMC), Amsterdam, handled by Enrico Ferrero, difference between the samples: swollen joint count (4 versus 9) and swelling (low versus high)

#### Is it a good pilot study? If not, what could be changed to make it better?
it's good that a lot of factors are the same for the samples, so there are less confounding factors that we need to take into account

#### What is the difference between fastQC and MultiQC?
Initial quality control (of raw data) versus summary of pipeline

#### What's the initial sample quality?
okay, but a lot of adapter sequence

#### Do we need to trim the data?
yes

#### What does the trimming do?
removes the adapter, shortens the reads

#### What additional information does the MultiQC report contain?
output of the other processes

#### Does it make sense to proceed with the analysis?
Depends on the goal of the pilot. To check the workflow from sample extraction to analysis, yes. To get information on differential methylation between high and low joint swelling, no.

## Further analyses:

#### Run the samples in methylKit. There is a good workflow with description on bioconductor.

# Client report:
What should be included in the report? Do we have all the data we need?

Write down comments here:

Summary of project
Take into account your PI
Processing report
Diagnostics
Caveats