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Creating a new submission
You have finished your analysis and now you want to share your data. Mothur can help!
1. The first command you want to run is get.mimarkspackage. The get.mimarkspackage command helps you fill provide all the necessary experimental data about your samples. Here is a link to information about the different mimarks packages, http://www.mothur.org/wiki/MIMarks_Data_Packages.
2. Create a project file. You can download a template here.
3. Run the make.sra command. This command will parse your sff or fastq file and generate an xml file for submission.
4. Email the SRA at NCBI (firstname.lastname@example.org) to let them know you are making a submission using mothur created files and need an aspera key or ftp instructions. They will provide you with instructions from there.