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.

Input

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.