EEB BootCamp 2020 - Revision history

imported>Lab: /* Bioinformatics tools for genomic epidemiology */

2020-08-06T03:00:40Z

Bioinformatics tools for genomic epidemiology

← Older revision		Revision as of 03:00, 6 August 2020
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	</syntaxhighlight>		</syntaxhighlight>
	* Sequence format converter [https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html Web tool]		* Sequence format converter [https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html Web tool]
	* TCS: To ~~infer~~ Haplotype network, TCS.jar file is provided in the dataset folder below, Required Java. [https://pubmed.ncbi.nlm.nih.gov/11050560/ PubMed link]		* TCS: To build Haplotype network, TCS.jar file is provided in the dataset folder below, Required Java. [https://pubmed.ncbi.nlm.nih.gov/11050560/ PubMed link]
	* Web-interactive visualization of Haplotype Network with tcsBU [https://cibio.up.pt/software/tcsBU/index.html Web tool]; [https://academic.oup.com/bioinformatics/article/32/4/627/1744448 Paper]		* Web-interactive visualization of Haplotype Network with tcsBU [https://cibio.up.pt/software/tcsBU/index.html Web tool]; [https://academic.oup.com/bioinformatics/article/32/4/627/1744448 Paper]
	* library(ggplot2) (R)		* library(ggplot2) (R)

imported>Lab: /* CoV genome data set */

2020-08-05T21:55:57Z

CoV genome data set

← Older revision		Revision as of 21:55, 5 August 2020
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	==CoV genome data set==		==CoV genome data set==
	* N=100 SARS-CoV-2 genomes collected during January, February & March 2020. Data source & acknowledgement [http://gisaid.org GIDAID] (<em>Warning: You need to acknowledge GISAID if you reuse the data in any publication</em>)		* N=100 SARS-CoV-2 genomes collected during January, February & March 2020. Data source & acknowledgement [http://gisaid.org GIDAID] (<em>Warning: You need to acknowledge GISAID if you reuse the data in any publication</em>)
	* Download the folder "bootcamp_august_6th_2020": [https://drive.google.com/file/d/~~1nRcj9iBUDEYJcf26ADze76pJDdbNzuGD~~/view?usp=sharing data file]		* Download the folder "bootcamp_august_6th_2020": [https://drive.google.com/file/d/1HBrHOJL3DIYrqzO0LIo7sdHvFbq4IZ3n/view?usp=sharing data file]
	* unzip the folder		* unzip the folder
	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>

imported>Lab: /* Tutorial */

2020-08-05T21:39:18Z

Tutorial

← Older revision		Revision as of 21:39, 5 August 2020
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	freq=read.table("cov_freq_by_continet.txt", sep = "\t")		freq=read.table("cov_freq_by_continet.txt", sep = "\t")
	colnames(freq)=c("position", "freq1", "freq2")		colnames(freq)=c("position", "freq1", "freq2")
			head(freq)

	ggplot(freq) +		ggplot(freq) +

imported>Lab: /* Tutorial */

2020-08-05T21:34:00Z

Tutorial

← Older revision		Revision as of 21:34, 5 August 2020
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	cut -f2,6 Europe_NA.frq \| tail -n +2 \| sed $'s/.://' > Europe_NA_minor.frq		cut -f2,6 Europe_NA.frq \| tail -n +2 \| sed $'s/.://' > Europe_NA_minor.frq
			less Europe_NA_minor.frq

	# calculate the SNPs frequency for Asia		# calculate the SNPs frequency for Asia

imported>Lab: /* Tutorial */

2020-08-05T21:08:07Z

Tutorial

← Older revision		Revision as of 21:08, 5 August 2020
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	## rename the snp2 recode file		## rename the snp2 recode file

			ls -lrt
	mv snps2.vcf.recode.vcf snps2.vcf		mv snps2.vcf.recode.vcf snps2.vcf

imported>Lab: /* CoV genome data set */

2020-08-05T21:00:01Z

CoV genome data set

← Older revision		Revision as of 21:00, 5 August 2020
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	* View files		* View files
	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>
			cd bootcamp_august_6th_2020

	ls -lrt # long list, in reverse timeline		ls -lrt # long list, in reverse timeline

	ls cov_data # a folder of 100 CoV2 genomes in FASTA format, pairwise genome alignment sam		ls cov_data # a folder of 100 CoV2 genomes in FASTA format, pairwise genome alignment in sam format generated by bwa (or nucmer)
	# ~~and indexed~~ sorted bam files generated by ~~bwa (or nucmer) and~~ samtools		# Indexed sorted bam files generated by samtools

	# We skipped bwa (or nucmer) and samtools part of the tutorial for time constrain.		# We skipped bwa (or nucmer) and samtools part of the tutorial for time constrain.

imported>Lab: /* Tutorial */

2020-08-05T20:04:29Z

Tutorial

← Older revision		Revision as of 20:04, 5 August 2020
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	less cov_haplotypes.nexus		less cov_haplotypes.nexus

	#if by any chance you are unable to complete part 1 then please use backup "cov_haplotypes.nexus" file inside the "Output" folder for rest of the steps		#if by any chance you are unable to complete part 1
			#then please use backup "cov_haplotypes.nexus" file inside the "Output" folder for rest of the steps
	# Build haplotype network for the cov dataset		# Build haplotype network for the cov dataset

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	wc cov_freq_by_continet.txt		wc cov_freq_by_continet.txt

	#if by any chance you are unable to complete part 1 then please use backup "cov_freq_by_continet.txt" file inside the "Output" folder to make SNPs frequency plot		#if by any chance you are unable to complete part 1
			#then please use backup "cov_freq_by_continet.txt" file inside the "Output" folder to make SNPs frequency plot
	# SNPs frequency plot by Continent		# SNPs frequency plot by Continent

imported>Lab: /* Tutorial */

2020-08-05T20:03:32Z

Tutorial

← Older revision		Revision as of 20:03, 5 August 2020
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	less cov_haplotypes.nexus		less cov_haplotypes.nexus

	#if by any chance you are unable to complete part 1 then please use backup "cov_haplotypes.nexus" file for rest of the steps		#if by any chance you are unable to complete part 1 then please use backup "cov_haplotypes.nexus" file inside the "Output" folder for rest of the steps
	# Build haplotype network for the cov dataset		# Build haplotype network for the cov dataset

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	<syntaxhighlight lang='bash'>		<syntaxhighlight lang='bash'>

	# calculate the SNPs frequency ~~for~~ Europe and North America		# calculate the SNPs frequency in Europe and North America

	grep -E -- "North America\|Europe" metadata_cov.txt \| cut -f1 > Europe_NA.ids		grep -E -- "North America\|Europe" metadata_cov.txt \| cut -f1 > Europe_NA.ids
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	wc cov_freq_by_continet.txt		wc cov_freq_by_continet.txt

	#if by any chance you are unable to complete part 1 then please use backup "cov_freq_by_continet.txt" file ~~for plotting~~		#if by any chance you are unable to complete part 1 then please use backup "cov_freq_by_continet.txt" file inside the "Output" folder to make SNPs frequency plot
	# SNPs frequency plot by Continent		# SNPs frequency plot by Continent

imported>Lab: /* Tutorial */

2020-08-05T20:00:31Z

Tutorial

← Older revision		Revision as of 20:00, 5 August 2020
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	bcftools reheader -s rename_ids.txt snps2.vcf > snps3.vcf		bcftools reheader -s rename_ids.txt snps2.vcf > snps3.vcf
	less snps3.vcf		less snps3.vcf
			</syntaxhighlight>

			* 2:55-3:10: Part 2: Build and interactive visualize haplotype network with TCS and tcsBU

			<syntaxhighlight lang='bash'>
	#create fasta file of snps		#create fasta file of snps

	cat rename_ids.txt \| while read line; do echo ">$line"; bcftools query -s "$line" -f '[%TGT]' snps3.vcf; echo; done > cov_haplotypes.fas		cat rename_ids.txt \| while read line; do echo ">$line"; bcftools query -s "$line" -f '[%TGT]' snps3.vcf; echo; done > cov_haplotypes.fas
	grep ">" cov_haplotypes.fas \| wc		grep ">" cov_haplotypes.fas \| wc
	~~</syntaxhighlight>~~

	* 2:55-3:10: Part 2: Build and interactive visualize haplotype network with TCS and tcsBU

	~~<syntaxhighlight lang='bash'>~~
	# Preparing files for haplotype network visualization by parsing the cov metadata		# Preparing files for haplotype network visualization by parsing the cov metadata
	# create file for geographic information		# create file for geographic information

imported>Lab: /* CoV genome data set */

2020-08-05T19:59:46Z

CoV genome data set

← Older revision		Revision as of 19:59, 5 August 2020
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	# We skipped bwa (or nucmer) and samtools part of the tutorial for time constrain.		# We skipped bwa (or nucmer) and samtools part of the tutorial for time constrain.
	#The bash script used to generate these files is available ~~if needed~~		#The bash script "sam-align-genome.bash" used to generate these files is available in the bootcamp_august_6th_2020 folder

	ls cov_data/*sorted.bam \| wc # 100 sorted.bam files correspond to 100 sequence files		ls cov_data/*sorted.bam \| wc # 100 sorted.bam files correspond to 100 sequence files