chemistry.md

The correspondence between chemistry and kits

• scopeV1 : Micro Bead Kit. This kit is no longer in use.
• scopeV2.*.* : Magnetic Bead Kit V1.
• scopeV3.*.* : Magnetic Bead Kit V2.

Analyze data with the updated chemistry version: scopeV3.0.1

• If you are using the latest CeleScope version(>= v1.5.2), it can auto-detect scopeV3.0.1, so --chemistry auto will work. You can also explicitly specify --chemistry scopeV3.0.1.

• If you are using CeleScope version < v1.5.2, then you need to use --chemistry customized and provide 3 additional arguments: (pattern, whitelist, linker).

multi_rna \
 --chemistry customized \
 --pattern C9L16C9L16C9L1U12T18 \
 --whitelist celescope/data/chemistry/scopeV3.0.1/bclist \
 --linker celescope/data/chemistry/scopeV3.0.1/linker_4types \
 ...

• There are no changes in other arguments.

Where to find pattern, whitelist and linker of each chemistry?

• pattern: https://github.com/singleron-RD/CeleScope/blob/master/celescope/tools/__init__.py
• whitelist and linker: https://github.com/singleron-RD/CeleScope/tree/master/celescope/data/chemistry/ . bclist is the barcode whitelist.