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## Vibrio cholerae typing from Illumina data | ||
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This is a guide for taking reads generated on an Illumina sequencer and mapping them against specific genes (_ctxA_, _wbeO1_, _wbfO139_, _tcpA_ classical, _tcpA_ El Tor, _toxR_) for the purpose of determining sample serotype. | ||
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## Setting up your working directory | ||
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This script assumpes the following: | ||
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* That you have already set up your working directory as described in the [assembly instructions](https://github.com/HopkinsIDD/illumina-vc/blob/main/instruction.md). Make sure you know where the raw fastq files are stored and make sure they follow the [naming convention](https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/NamingConvention_FASTQ-files-swBS.htm) | ||
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* That the `scripts` folder inside your working directory contains the `map_genes.sh` script. | ||
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* That all six gene-specific reference FASTAs are contained in a directory called `typing`. If you cloned this git repository, these reference files can be found in `ref_genomes/typing`. | ||
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Once you have the required files in your working directory, navigate to this directory and create a new folder where you will store your typing results: | ||
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``` | ||
cd my-project | ||
``` | ||
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``` | ||
mkdir typing_results | ||
``` | ||
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## Running the typing script | ||
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Run the typing script as follows: | ||
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``` | ||
bash scripts/map_genes.sh sample-name my-project path-to-raw-data num-lanes num-cores ref-dir output-dir | ||
``` | ||
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Where `sample-name` is the 'SampleName' prior to '_L00...' in your fastq files,`my-project` is the absolute path to your project directory, and `path-to-raw-data` is the path to your raw fastq files. `num-lanes` is the number of lanes you used to run this sample. `num-cores` should be less or equal to [the number of processors on your computer](https://github.com/HopkinsIDD/illumina-vc/blob/main/instruction.md/#determining-the-number-of-processors-on-your-computer).`ref-dir` should be the directory that contains the gene-specific FASTA files (usually `my-project/ref_genomes/typing`). `output-dir` will be the folder to store typing results (`my-project/typing_results`). | ||
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## Evaluating typing results | ||
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The typing script will produce one output file (`samplename_typing_summary.txt`). This file will look something like this: | ||
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``` | ||
SAMPLENAME gene reads_mapped reads frac_mapped mean_depth pos_covered total_pos frac_covered | ||
ERR3039943 ctxA 96 588182 .0001632 27.4582 777 777 1.0000000 | ||
ERR3039943 tcpA_classical 87 588182 .0001479 9.74046 1048 1048 1.0000000 | ||
ERR3039943 tcpA_eltor 96 588182 .0001632 28.3126 675 675 1.0000000 | ||
ERR3039943 toxR 134 588182 .0002278 30.8923 891 891 1.0000000 | ||
ERR3039943 wbeO1 3660 588185 .0062225 38.4333 21122 21122 1.0000000 | ||
ERR3039943 wbfO139 1923 588187 .0032693 9.17084 46721 46721 1.0000000 | ||
``` | ||
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These files may be easier to view in a spreadsheet software such as Excel. |