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

3KB

mc-V2.mouse.mapping_config.ini

Open

snmC-seq3, Mouse, V2 barcode

3KB

mct-V2.mouse.mapping_config.ini

Open

snmCT-seq, Mouse, V2 barcode

3KB

m3c-V2.human.mapping_config.ini

Open

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.