Stefan Schattgen
Stefan Schattgen
Having the same issue installing from source.
The solution above was not working for all cases for me so I wrote a little R code that reformats the mixcr outputs so that they work with vdjtools convert....
I had vdjtools installed (and working) via homebrew before but I was having a bunch of problems with xcode and R packages so I uninstalled vdjtools in my attempts to...
PathLike was implemented in 3.6 so I'm not sure if that's the issue. https://docs.python.org/3/library/os.html#os.PathLike Nonetheless, you can certainly try moving up in version and see if that helps. I use...
Hi, You're correct that the issue is due to a misalignment between barcodes in TCR and GEX. There was likely some sort of alteration in the GEX barcode during integration...
Hi Guillem, Thanks for your interest. The issue is due to the nucleotide sequence not being equal to 3 times the amino acid sequence. It seems you have extra/missing nucleotides...
Hi Leeana, Thanks for your interest in conga. The code was originally tailored to a specific dataset, but with a little modification, you should be able to apply these functions...
Hi! Phil be me to the punch while I was putting it together, but I figured I'd share mine too. It's a nearly identical solution but intended for use in...
'TRAV13-4-DV7*01','TRAV15D-1-DV6D-1*01','TRAV15-2-DV6-2*01','TRAV15D-2-DV6D-2*01','TRAV6-7-DV9*01','TRAV15-1-DV6-1*01'
'TRAV13-4-DV7*01','TRAV15D-1-DV6D-1*01','TRAV15-2-DV6-2*01','TRAV15D-2-DV6D-2*01','TRAV6-7-DV9*01','TRAV15-1-DV6-1*01'