Nathan Edwards

Does anyone have any insight on this? This is blocker for my SMW site. Is there a way to manipulate the #ask: to eliminate this issue? Based on my exploration,...

I just checked the database query (SQLStore) itself (as shown by the debug option on semantic search), and as far as I can tell, the chained properties logic is implemented...

@Seb35 Awesome! Thanks for your work on this. I will attempt a monkey patch ASAP.

By eye, I think the issue with not checking multiple potential parents is still likely to be an issue, but I guess I'll have to find another example to demonstrate...

Its seems like the two pieces of code Glycan.iterconfiguration and AmbigousLink.find_open_position are kinda implementing the same logic, though in different ways. I didn't like the ambiguous position implementation or the...

Hi @singcell . SCReadCounts can certainly give you cell-specific and allele-specific UMI (or read)-counts given prior knowledge of the distinguishing loci. You would prepare your SNV file to describe the...

Do you know the loci on the reference genome that indicate maternal vs paternal expression? If so, you can make the required SNV input file. Lines look like this: CHR#...

Hi @Giovanna0806! Thank you for your interest in SCExecute. You will need a BAM file produced by STARsolo or CellRanger when it aligns your sequences against the reference, which also...

@Giovanna0806: Pasting the email reply in here so I don't lose track of it Thank you for the help! I confirm that I have the .BAM file generated by aligning...

Unless you want to keep the cell-specific bamfiles around, you can omit the --filetemplate argument. I suggest you create a shell script to capture the details of how you want...