11. IHEC standard analyses¶
To perform a standard IHEC WGBS analysis it is necessary to have an up-to-date version of gemBS installed, and to set the analysis parameters appropriately. To help with the configuration issue, gemBS includes standard configuration files that can be included in the parameter configuration files to ensure that the standard pipeline behaviour is achieved.
The gemBS distribution includes three IHEC analysis configuration files:
IHEC_standard.conf IHEC_RRBS.conf IHEC_PBAT.conf
An example configuration file that uses
IHEC_standard.conf can be seen here: Example configuration file.
The position of the
include statement in the configuration file is important: variables must be included before they
are referenced, and new variable definitions will overwrite existing definitions.
Once the parameter files have been set up, then running the standard set of gemBS commands (map, call, extract, map-report and call-report) will perform the standard pipeline and generate the required outputs.
11.1. IHEC standard configuration files¶
We can see the contents of the three files below:
[index] sampling_rate = 4 [mapping] non_stranded = False remove_individual_bams = True [calling] mapq_threshold = 10 qual_threshold = 13 reference_bias = 2 left_trim = 5 right_trim = 0 keep_improper_pairs = False keep_duplicates = False haploid = False conversion = auto remove_individual_bcfs = True # Contigs smaller than contig_pool_limit will be called together contig_pool_limit = 25000000 [extract] strand_specific = True phred_threshold = 10 make_cpg = True make_non_cpg = True make_bedmethyl = True make_bigwig = True
include IHEC_standard.conf [calling] keep_duplicates = True
include IHEC_standard.conf [mapping] non-stranded = True [calling] keep_improper_pairs = True
We can see that the
IHEC_PBAT.conf configuration files are simply slight modifications of the
IHEC_standard.conf file, obtained by
including the standard file and then overwriting key parameters.
11.2 Use of gemBS containers¶
To ensure that gemBS is installed correctly and is up-to-date, it can be convenient to make use of containerized versions of gemBS (Singularity or Docker). This simplifies the installation process and makes sure that the support libraries and applications needed by gemBS are installed correctly and are the right versions (see 10. Containers for more details).