Prepare Mapping Config

Prepare a config file that contains all parameters and path to the genome reference

Related Commands
# Print out template of the mapping config
yap default-mapping-config
Purpose
In this step, you need to prepare a MappingConfig file that contains all the parameters for the mapping pipeline. Mainly, the path to the genome reference files.
​What is the MappingConfig file?​
Input
All the genome reference files, see how to prepare here.
Technology type
Barcoding version
Step 1 - Get a template of MappingConfig
yap default-mapping-config -h
​
usage: yap default-mapping-config [-h] --mode {mct,mc} --barcode_version
                                  {V1,V2} --bismark_ref BISMARK_REF
                                  --genome_fasta GENOME_FASTA
                                  [--star_ref STAR_REF] [--gtf GTF] [--nome]
​
optional arguments:
  -h, --help            show this help message and exit
  --mode {mct,mc}       Library mode (default: None)
  --barcode_version {V1,V2}, -v {V1,V2}, -V {V1,V2}
                        Barcode version, V1 for 8 random index, V2 for 384
                        random index (default: None)
  --bismark_ref BISMARK_REF
                        Path to the bismark reference (default: None)
  --genome_fasta GENOME_FASTA
                        Path to the genome fasta file (default: None)
  --star_ref STAR_REF   [mct only] Path to the STAR reference, required if
                        mode is mct (default: None)
  --gtf GTF             [mct only] Path to the GTF annotation file, required
                        if mode is mct (default: None)
  --nome                Does this library have NOMe treatment? (default:
                        False)
Example of MappingConfig files
mc-V2.mouse.mapping_config.ini
3KB
Binary
snmC-seq3, Mouse, V2 barcode
mct-V2.mouse.mapping_config.ini
3KB
Binary
snmCT-seq, Mouse, V2 barcode
m3c-V2.human.mapping_config.ini
3KB
Binary
snm3C-seq, Human, V2 barcode
Step 2 - Review
Review and modify the MappingConfig template as you need, each parameter is explained within the template.
Remember different server needs different MappingConfig (different reference path).
Output
mapping_config.ini file, needed for yap demultiplex.

Prepare PlateInfo & bcl2fastq SampleSheet

Prepare Reference Files

Last modified 2yr ago