Snpcallphylo - Revision history

Rf at 16:01, 26 August 2016

2016-08-26T16:01:30Z

2016-08-26T16:00:15Z

2016-08-26T15:39:15Z

Created page with "= Introduction = Cosmika Goswami's pipeline for call SNPs on prokaryotic NGS data."

New page

= Introduction =

Cosmika Goswami's pipeline for call SNPs on prokaryotic NGS data.

← Older revision		Revision as of 16:01, 26 August 2016
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	* Copy the snpcallphylo python executable into it and create two subfolders: input and output. You can also choose other names.		* Copy the snpcallphylo python executable into it and create two subfolders: input and output. You can also choose other names.
	* either copy or symlink you data files into the input directory		* either copy or symlink you data files into the input directory
		+	* You can start to create the "configuration.ini" file first .. it needs to specify the input files. Here is a an awk commandline which will let you do that:
		+
		+	ls -1 `pwd`/data/*.fastq.gz \| awk '{split($0,a,"/");;split(a[9],b,"_"); print b[1]"_"b[4]"="$0}'

← Older revision		Revision as of 16:00, 26 August 2016
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	Cosmika Goswami's pipeline for call SNPs on prokaryotic NGS data.		Cosmika Goswami's pipeline for call SNPs on prokaryotic NGS data.
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		+	= Procedure =
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		+	* It is best to create a dedicated folder/directory in which you will carry out your work
		+	* Copy the snpcallphylo python executable into it and create two subfolders: input and output. You can also choose other names.
		+	* either copy or symlink you data files into the input directory