search

frisen-lab / TREX

Simultaneous lineage TRacking and EXpression profiling of single cells using RNA-seq
MIT License
5 stars 6 forks source link

Reconsider the name of the `annotations` folder and its contents #12

Closed marcelm closed 2 years ago

marcelm commented 2 years ago

I’ve moved this to-do item to a separate issue so the discussion can be kept separate.

The folder name annotations/ isn’t quite accurate. I chose it only because I had to come up with something quickly: The H2b-EGFP-30N-LTR.fa file in it isn’t annotation. The commonality between the two files is that they are needed to reproduce the results from the paper, so a name reflecting that may be better. (I still cannot come up with anything better, though ...)

You said that all available annotations should be moved to that folder. Which ones would these be? We have the chrTomato-N.fa and chrTomato-N.gtf files, but are these relevant for anyone?

Leonievb commented 2 years ago

Yes, these files are relevant for those who want to follow up each step of the paper including merging the extra chromosome into the reference genome with cellranger mkref. So what about calling this folder references? Plus, to be complete, I would add the chrTomato-N.fa and chrTomato-N.gtf to this folder too. Or is it not a good ideas to have files doublets?

marcelm commented 2 years ago

Perfect! I have renamed the folder now and copied the chrTomato* files into it.

Do we need the chrTomato* files in tests/data/ at all? The tests run without them. But having copies would be ok in this limited case.

Leonievb commented 2 years ago

no, we actually don't need it there at all. Whoever is interested in learning how to prepare for the cellranger run, will not look into this folder to find the references

marcelm commented 2 years ago

Good, I will move the files instead of copying them.