apredeus
commented
1 year ago Hi Carles,
Thank you for your nice words! Most of the scripts here are Sanger Institute - specific, and the reference location is on our compute cluster and not available to public. However, they are very easy to re-create - just follow Cell Ranger instructions for the reference you want that can be found here, but instead of the final cellranger mkref command run a STAR --genomeGenerate etc (I don't remember the exact syntax but you get the idea).
I will update the README on the scripts that have been deleted, thank you for catching that.
Cheers -- Alex
Hi!
I've been writing a wrapper script for STARsolo and bumped into your GitHub repo. Very nice implementation and great explanations!
I found a couple issues on your README file that maybe you would like to update:
Under section Processing scRNA-seq with STARsolo, subsection 10X: reproducing Cell Ranger v4 and above (but much faster) you mention some scrips for specific 10X chemistries that no longer exist. It looks like you replaced them with a single script that automatically detects the correct chemistry.
Under section Reference genome and annotation, subsection Pre-made reference location you mention available pre-made genome references and whitelists. Are those public? If so, it's not clear where to obtain them. I'm guessing they are only available for internal use. Maybe you could clarify this?
Thank you! Carles