MAGNIFIER

• Methyltransferase accessible genome region finder (MAGNIFIER) is a bioinformatic tools designed for nanopore-based chromatin methylatransferase accessible chromatin detection.

Dependencies

• Python version >= 3.7
• numpy version >= 1.19.2
• pandas version >= 1.2.1
• pysam version >= 0.15.3
• megalodon version >= 2.2.9
• pybedtools version >= 0.8.1
• scipy version >= 1.6.0

Installation instructions

Installing the latest code from github (recommended)

You can download and compile the latest code from github as follows:

git clone https://github.com/Goatofmountain/MAGNIFIER.git

Usage

Example Usage

Data prepare

• We recommand a megalodon methylation base calling pipeline for Case and Control sample before MAGNIFIER calculation (megalodon: https://github.com/nanoporetech/megalodon)

For CG and A motifs

megalodon <fast5 file dir> --outputs mappings mod_mappings mods --reference <Human reference> --devices 0 1 2 3 --processes 40 --guppy-server-path <Path to guppy_basecall_server> --guppy-params -d <basecallmodels Dir> --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --overwrite --mod-min-prob 0 --output-directory ./megalodon_CG_A --mod-motif Z CG 0 --mod-motif Y A 0

For GC motif

megalodon <fast5 file dir> --outputs mappings mod_mappings mods --reference <Human reference> --devices 0 1 2 3 --processes 40 --guppy-server-path <Path to guppy_basecall_server> --guppy-params -d <basecallmodels Dir> --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --overwrite --mod-min-prob 0 --output-directory ./megalodon_GC --mod-motif Z GC 1

• Then using our main script to calculate the chromatin accessibility:

python MAGNIFIER.py -c config.config

• All parameter should be written into the configure file (config.config). The example configure file could be found in this Repostories with path: ./example/ExampleTXT.config
• Detailed config file annotation is represent as follow:

[AimDBList]
CaseDBList	=	<Dir path to megalodon_db1 of Case Data>,<Dir path to megalodon_db2 of Case Data>
ControlDBList	=	<Dir path to megalodon_db1 of Control Data>,<Dir path to megalodon_db2 of Control Data>

[BaseLabel]
ModBaseList	=	<base marker character for megalodon_db1>;<base marker character for megalodon_db2>        # Y means A, Z means C, multiple base maker in one database should be seperated with ",", eg. Y,Z means both A and C base modification profile is in this megalodon database 
AimBaseList	=	<mod-base motif character for megalodon_db1>;<mod-base motif character for megalodon_db2>  # ordered according to the ModBaseList, you can choose m6A, CpG, and GpC. Same as ModBaseList multiple mod-base motif should be seperated with ",", eg. m6A,CpG

[outDir]
CaseBedDir	=	<TMP bed dir for megalodon_db1 of Case Data>,<TMPbed dir for megalodon_db2 of Case Data>
ControlBedDir	=	<TMP bed dir for megalodon_db1 of Control Data>,<TMPbed dir for megalodon_db2 of Control Data>
PerReadOutDir	=	<Per-read Z status data output dir>
SignalOutDir	=	<Final Result output dir>

[AttachFiles]
RefFile = <abstract path to reference genome fasta file>
RegionFile	=	<abstract path to interested genome region in bed format> 

• Please firstly run the following example program to check whether all package is ready to work.

cd ./example
python MAGNIFIER_Example.py -h