CellRanger TCR/BCR IMGT 최신버전으로 ref만들고 돌리기

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🔗 Building a custom reference for V(D)J using IMGT tool

• IMGT에서 최신 데이터 다운받아서 reference만들어줌.

source the environment of Cell Ranger for your shell (bash/csh)

(for bash shell)

source /sc/arion/projects/scMultiscale/chos14/source/cellranger-10.0.0/sourceme.bash

python –version

Using a script that comes with Cell Ranger, get data from IMGT and create a FASTA suitable for use by mkvdjref

The option –species is the name of the species for which the data is to be downloaded.

The option –genome provides the prefix used to name the 2 output files. Only the file with the suffix -mkvdjref-input.fasta is used as input to the mkvdjref utility.

/sc/arion/projects/scMultiscale/chos14/source/cellranger-10.0.0/lib/bin/fetch-imgt –genome vdj_IMGT_human –species “Homo sapiens”

Build the CR reference. could also include Cell Ranger on your PATH to avoid specifying the full path for cellranger.

The option –genome is a single identifier with no special symbols aside from hyphen or underscore. The reference will be placed in a directory created with that name.

The option –seqs is the mkvdjref-input.fasta file generated by the fetch-imgt command.

/sc/arion/projects/scMultiscale/chos14/source/cellranger-10.0.0/cellranger mkvdjref –genome=vdj_IMGT_human –seqs=vdj_IMGT_human-mkvdjref-input.fasta