Whole genome alignment pipeline - Revision history

Dawes0011 at 09:01, 16 June 2023

2023-06-16T09:01:16Z

← Older revision		Revision as of 11:01, 16 June 2023
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	<pre>Warning in install.packages(new.packages) :		<pre>Warning in install.packages(new.packages) :
	'lib = "~~/cm~~/shared/apps/R/3.6.2/lib64/R/library"' is not writable</pre>		'lib = "/shared/apps/R/3.6.2/lib64/R/library"' is not writable</pre>
	Follow the instructions on how to install R packages locally [https://wiki.anunna.wur.nl/index.php/Installing_R_packages_locally here] and try to install the packages again.		Follow the instructions on how to install R packages locally [https://wiki.anunna.wur.nl/index.php/Installing_R_packages_locally here] and try to install the packages again.

Moiti001 at 13:56, 18 July 2022

2022-07-18T13:56:19Z

← Older revision		Revision as of 15:56, 18 July 2022
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	For up-to-date documentation see [https://github.com/CarolinaPB/whole-genome-alignment here]		For up-to-date documentation see [https://github.com/CarolinaPB/whole-genome-alignment here]

	= ~~Single Cell preprocessing~~ pipeline =		= Whole genome alignment pipeline =

	Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/whole-genome-alignment		Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/whole-genome-alignment

Moiti001 at 13:47, 18 July 2022

2022-07-18T13:47:58Z

← Older revision		Revision as of 15:47, 18 July 2022
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	OUTDIR: /path/to/outdir</syntaxhighlight>		OUTDIR: /path/to/outdir</syntaxhighlight>
	* GENOME: path to the genome fasta file (can be compressed). This is the genome that you want to be compared to all the others		* GENOME: path to the genome fasta file (can be compressed). This is the genome that you want to be compared to all the others
	* COMPARISON_GENOME: genome for whole genome comparison. Add your species name and the path to the fasta file. ex: chicken: /path/to/chicken.fna.gz. You can add several genomes, one on each line.		* COMPARISON_GENOME: genome fasta (can be compressed) for whole genome comparison. Add your species name and the path to the fasta file. ex: chicken: /path/to/chicken.fna.gz. You can add several genomes, one on each line.
	* MIN_ALIGNMENT_LENGTH and MIN_QUERY_LENGTH - parameters for plotting. If your plot is coming out blank or if there’s an error with the plotting step, try lowering these thresholds. This happens because the alignments are not large enough.		* MIN_ALIGNMENT_LENGTH and MIN_QUERY_LENGTH - parameters for plotting. If your plot is coming out blank or if there’s an error with the plotting step, try lowering these thresholds. This happens because the alignments are not large enough.
	* PREFIX: name of your species (ex: turkey)		* PREFIX: name of your species (ex: turkey)

Moiti001: added documentation

2022-07-18T13:46:02Z

added documentation

New page

Author: Carolina Pita Barros 
Contact: carolina.pitabarros@wur.nl 
ABG 

For up-to-date documentation see [https://github.com/CarolinaPB/whole-genome-alignment here]

= Single Cell preprocessing pipeline =

Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/whole-genome-alignment


== First follow the instructions here: ==

[https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Step by step guide on how to use my pipelines] 
Click [https://github.com/CarolinaPB/snakemake-template/blob/master/Short%20introduction%20to%20Snakemake.pdf here] for an introduction to Snakemake


== ABOUT ==

This pipeline aligns one or more genomes to a specified genome and plots the alignment.


==== Tools used: ====

* [https://github.com/lh3/minimap2 minimap2]
* R
** [https://github.com/tpoorten/dotPlotly/blob/master/pafCoordsDotPlotly.R pafCoordsDotPlotly.R]

{|
!align="center"| [[File:whole-genome-alignment-workflow.png]]
|-
|align="center"| ''Pipeline workflow''
|}


=== Edit config.yaml with the paths to your files ===

<syntaxhighlight lang="yaml"># genome alignment parameters:
GENOME: /path/to/genome #genome fasta to be compared
COMPARISON_GENOME:
<genome1>: path/to/genome1.fasta
<genome2>: path/to/genome2.fasta
<genome3>: path/to/genome3.fasta

# filter alignments less than cutoff X bp
MIN_ALIGNMENT_LENGTH: 10000
MIN_QUERY_LENGTH: 50000

PREFIX: <prefix>

OUTDIR: /path/to/outdir</syntaxhighlight>
* GENOME: path to the genome fasta file (can be compressed). This is the genome that you want to be compared to all the others
* COMPARISON_GENOME: genome for whole genome comparison. Add your species name and the path to the fasta file. ex: chicken: /path/to/chicken.fna.gz. You can add several genomes, one on each line.
* MIN_ALIGNMENT_LENGTH and MIN_QUERY_LENGTH - parameters for plotting. If your plot is coming out blank or if there’s an error with the plotting step, try lowering these thresholds. This happens because the alignments are not large enough.
* PREFIX: name of your species (ex: turkey)
* OUTDIR: directory where snakemake will run and where the results will be written to

If you want the results to be written to this directory (not to a new directory), comment out or remove

<pre>OUTDIR: /path/to/outdir</pre>

== ADDITIONAL SET UP ==


=== Installing R packages ===

First load R: <code>module load R/4.0.2</code>

Enter the R environment by writing <code>R</code> and clicking enter. Install the packages:

<pre>list.of.packages <- c("optparse", "data.table", "ggplot2")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)</pre>
If you get an error like this:

<pre>Warning in install.packages(new.packages) :
'lib = "/cm/shared/apps/R/3.6.2/lib64/R/library"' is not writable</pre>
Follow the instructions on how to install R packages locally [https://wiki.anunna.wur.nl/index.php/Installing_R_packages_locally here] and try to install the packages again.


== RESULTS ==

The most important files and directories are:

* '''<run_date>_files.txt''' dated file with an overview of the files used to run the pipeline (for documentation purposes)
* '''genome_alignment/{prefix}''vs''{species}.paf''' paf format file w