6.8 years ago by
I think naming conventions are always useful and essential when multiple persons are working on the same data. Nevertheless, the convention itself just needs to be one that everybody agrees to, provided that it is clear enough.
In my previous group we sequenced RNA but also a lot on chromatin modifications (ChIP-seq). Our naming convention was similar to your example, but we'd put the library right after the sample number, for more immediate recognition. We used mostly the same organism so we wouldn't add that tag to the file name, but add the developmental stage at which the run was performed. Read length was also mostly the same up to a point where we started decided to add it later for clarity. Transformations on the original file were generally added dot-separated, as such:
Anyway, sometimes you work so much in a project that almost everyone knows which sample has what just by the sample number.
Hope this was helpful.