When working in a server environment such as the two servers we will be using, we have a few tips on how to name files.

General Naming

Be descriptive in naming your files and directories. This will allow you to better understand what you did if you need to revisit a project several months later.

In particular, when running an analysis, it is helpful to either include the date you ran the analysis in its respective directory, such as 072021_bwa_trimming. Alternatively, you can number the directories in the order in which you performed the analysis, such as 3_bwa_trimming. In either case, this gives you a chronological order of what you performed for the sake of clarity and reproducibility.

No Spaces in Filenames

Using spaces in filenames makes things difficult in these environments, so we strongly discourage users from using them. Instead, we prefer to use a _ to make a file's name more legible.

• get primary sequences.py - Do not do this.
• getprimarysequences.py - Acceptable, but difficult to read.
• get_primary_sequences.py - Preferred naming scheme.
• getPrimarySequences.py - Also acceptable.

File Extensions

Always include a file extension when creating a file, especially if it contains data that will be used downstream in your analysis or contains commands that will be run to reproduce your data. File extensions tell you what to expect from a file, and this is essential for data reproducibility. If you have any questions about which extension to use, or if you find an extension you don't know, feel free talk to us about it.