how to do with complex barcodes or multi linked barcode

[d-jch]

Star has the solution:

More complex barcodes are activated with --soloType CB_UMI_Complex and are described with the following parameters

soloCBposition              -
strings(s)              position of Cell Barcode(s) on the barcode read.
                        Presently only works with --soloType CB_UMI_Complex, and barcodes are assumed to be on Read2.
                        Format for each barcode: startAnchor_startDistance_endAnchor_endDistance
                        start(end)Anchor defines the anchor base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end
                        start(end)Distance is the distance from the CB start(end) to the Anchor base
                        String for different barcodes are separated by space.
                        Example: inDrop (Zilionis et al, Nat. Protocols, 2017):
                        --soloCBposition  0_0_2_-1  3_1_3_8

soloUMIposition             -
string                  position of the UMI on the barcode read, same as soloCBposition
                        Example: inDrop (Zilionis et al, Nat. Protocols, 2017):
                        --soloUMIposition  3_9_3_14

soloAdapterSequence         -
string:                 adapter sequence to anchor barcodes.

soloAdapterMismatchesNmax   1
int>0:                  maximum number of mismatches allowed in adapter

also it has options to provide multiple white list coresponding to the barcodes:

--soloCBwhitelist
default: -
string(s): file(s) with whitelist(s) of cell barcodes. Only –soloType CB_UMI_Complex allows more than one whitelist file.
None no whitelist: all cell barcodes are allowed

[DongzeHE]

Hi @d-jch Pleae check the document of EGFDL

Basically, you can specify custom chemistry specification in simpleaf. You can also save those chemistries for future use using simpleaf chemistry subcommands.