Hi,
when I run simpleaf flex-quant --chemistry 10x-flexv2-gex-3p (as in #191) I retrieve 8 cells which is short of the 13k I get with cellranger. After checking the chemistry geometry definition (1{b[16]u[12]x[10]s[10]}2{r:}) and comparing with the expected output from 10x flex v2 (page 119 here): -N16-N12-N(0,3)-TTGCTAGGACCG-BC10- I think the correct geometry should be 1{b[16]u[12]x[10-13]s[10]x:}2{r:} (or maybe: 1{b[16]u[12]x[0-3]f[TTGCTAGGACCG]s[10]x:}2{r:}). So it can be now of variable length, which is different to flex v1 which was constant (page 95 here).
If I manual change the geometry in the chemistry.json file I get this error:
Error: unknown geometry '1{b[16]u[12]x[0-3]f[TTGCTAGGACCG]s[10]x:}2{r:}' (not a built-in name, and custom parse failed: invalid length '0-3' at position 12)
Hi,
when I run
simpleaf flex-quant --chemistry 10x-flexv2-gex-3p(as in #191) I retrieve 8 cells which is short of the 13k I get with cellranger. After checking the chemistry geometry definition (1{b[16]u[12]x[10]s[10]}2{r:}) and comparing with the expected output from 10x flex v2 (page 119 here):-N16-N12-N(0,3)-TTGCTAGGACCG-BC10-I think the correct geometry should be1{b[16]u[12]x[10-13]s[10]x:}2{r:}(or maybe:1{b[16]u[12]x[0-3]f[TTGCTAGGACCG]s[10]x:}2{r:}). So it can be now of variable length, which is different to flex v1 which was constant (page 95 here).If I manual change the geometry in the chemistry.json file I get this error: