Commit 64d85853 authored by Noort, Maite van den's avatar Noort, Maite van den
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Update README.md

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# Maite internship epiGBS
All code written for testing the reproducibility and reliability of epiGBS2
# Rscripts_uniqueReads
Here are scripts that makes ggplots from the number of unique reads.
## - unique_reads_lib1.R
- Author: Maite van den Noort
- Date: 19-11-2020
- Function: This script makes different graphs of the number of reads who are unique from library 1.
## - unique_reads_lib2.R
- Author: Maite van den Noort
- Date: 19-11-2020
- Function: This script makes different graphs of the number of reads who are unique from library 2.
# Rscripts_duplication
Here are scripts that makes ggplots from the number of duplicated reads. And scripts that makes ggplots of percentage duplicated reads.
## - duplications_percentage_lib1.R
- Author: Maite van den Noort
- Date: 19-11-2020
- Function: This script makes different graphs of the percentage reads who are duplicated from library 1.
## - duplications_percentage_lib2.R
- Author: Maite van den Noort
- Date: 19-11-2020
- Function: This script makes different graphs of the percentage reads who are duplicated from library 2.
## - duplication_reads_lib1.R
- Author: Maite van den Noort
- Date: 19-11-2020
- Function: This script makes different graphs of the number of reads who are duplicated from library 1.
## - duplication_reads_lib2.R
- Author: Maite van den Noort
- Date: 19-11-2020
- Function: This script makes different graphs of the number of reads who are duplicated from library 2.
# Rscripts_methylation
Here are all the scripts that do something with methylation
## - ScriptsMaarten.R
- Author: Maarten Postuma (edited by: Maite van den Noort)
- Date: unknown (date edited: 19-11-2020)
- Function: This script makes different graph to compare two methylation.bed files with each other (made with the same reference or denovo).
# Rscripts_barcodes
Here are all the scripts making ggplots about the reatained reads (barcodes)
## - Retained_barcodes_samplenames.R
- Author: Maite van den Noort
- Date: 30-12-2020
- Function: This script makes ggplots about the retained reads per sample
## - Retained_barcodes_lollipop.R
- Author: Maite van den Noort
- Date: 07-01-2021
- Function: This script makes a lollipop plot about the retained reads. Watson and crick are here together.
The samplenames are on y-as with the two librarys in the plot.
- use in report
## - Retained_barcodes_lib1.R
- Author: Maite van den Noort
- Date: 11-12-2020
- Function: This script makes ggplots about the retained reads for library 1
## - Retained_barcodes_lib2.R
- Author: Maite van den Noort
- Date: 11-12-2020
- Function: This script makes ggplots about the retained reads for library 2
## - Retained_barcodes_lib1_and_lib2.R
- Author: Maite van den Noort
- Date: 30-12-2020
- Function: This script makes ggplots about the retained reads for library 1 and 2
## - Retained_barcodes_combined_samplenames.R
- Author: Maite van den Noort
- Date: 07-01-2021
- Function: This script makes ggplots about the retained reads for library 1 and 2. Watson and crick are here together.
This is also showed per sample
- use in report
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