Prepare Mapping Config

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

# 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)