Input when running RDscan

[stuber]

What is the exact input to provide to the command below when trying to determine the RD regions of a sample? Is the working directory to contain the files to be analyzed? Please provide examples if possible. Thanks,

snakemake --conda-frontend mamba --use-conda -j {Number of cores}

[dbespiatykh]

You should configure workflow as described here: https://github.com/dbespiatykh/RDscan/tree/master/config.
In short, you need to add your samples to RDscan/config/samples.tsv like so:

Run_accession	R1	R2
your_sample_A	/path/to/your_sample_A_1.fastq.gz	/path/to/your_sample_A_2.fastq.gz
your_sample_B	/path/to/your_sample_B_2.fastq.gz	/path/to/your_sample_B_2.fastq.gz

Then you need to run the command you mentioned (inside RDscan directory).
Alternatively, you can use this command (to omit mamba): snakemake --cores all --use-conda.

[stuber]

Thanks! From: Dmitry Bespiatykh ***@***.***> Date: Tuesday, May 2, 2023 at 2:44 PM To: dbespiatykh/RDscan ***@***.***> Cc: Stuber, Tod - MRP-APHIS ***@***.***>, Author ***@***.***> Subject: Re: [dbespiatykh/RDscan] Input when running RDscan (Issue #3) You should configure workflow as described here: https://github.com/dbespiatykh/RDscan/tree/master/config. In short, you need to add your samples to RDscan/config/samples.tsv like so: Run_accession R1 R2 your_sample_A /path/to/your_sample_A_1.fastq.gz /path/to/your_sample_A_2.fastq.gz your_sample_B /path/to/your_sample_B_2.fastq.gz /path/to/your_sample_B_2.fastq.gz Then you need to run the command you mentioned (inside RDscan directory). Alternatively, you can use this command (to omit mamba): snakemake --cores all --use-conda.