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Sufficient information to run the pipeline #1
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Hello, Thanks for the custom pipelines and for this nice protocol! On a similar note, I'm having trouble understanding the exact input I should use to run the DNA-based pipeline. Would it be possible to give me a specific example? Please provide if possible an example samplesheet.csv file and also a specific value for the "--directory" parameter assuming that I already have my FASTQ files ready, so I don't need to run cellranger to produce them from the BCL files. Thanks in advance, |
Hello Maria, Here is an example of a few runs and how to set up the software. It assumes the fastq files are in the directory that bcl2fastq would create. So you need to make that path and put your fastq's in it if you don't have that path already. Create conda environment Download reference or use 10x cellranger references Make Directories Run pipeline <With BCL to fastq, may need to install bcl2fastq> Tim |
Dear authors,
Please provide information needed to execute your pipeline:
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