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
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
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
.
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