Difference between revisions of "Snpcallphylo"
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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 | ||
| + | * 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: | ||
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| + | ls -1 `pwd`/data/*.fastq.gz | awk '{split($0,a,"/");;split(a[9],b,"_"); print b[1]"_"b[4]"="$0}' | ||
Latest revision as of 16:01, 26 August 2016
Introduction
Cosmika Goswami's pipeline for call SNPs on prokaryotic NGS data.
Procedure
- 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
- 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}'
