Methylome transfer system

There are several commands within mxe and the best way to start is to understand the dnmtools roi command, as the information functionality provided by mxe is the same. If you need to learn about dnmtools roi you can find the docs here

Before starting, an index file is required. To make the index, you need the reference genome in a single fasta format file. If your reference file name is hg38.fa, then do this:

mxe index -v -g hg38.fa -x hg38.cpg_idx

If hg38.fa is roughly 3.0G in size, then you should expect hg38.cpg_idx to be about 113M in size.

The starting point within mxe is a file in the xcounts format that involves the symmetric CpG sites. This is called a symmetric xcounts format file, and may be gzip compressed, in which case the extension should be .xsym.gz. First I will explain how to start with this format, and below I will explain how to start with the other format used by dnmtools. We again assume that the reference genome is hg38.fa and that this file was used to create the SRX012345.xsym.gz file. This ensures a correspondence between the SRX012345.xsym.gz file and the hg38.cpg_idx file we will need. Here is how to convert such a file into the mxe format:

mxe compress -v -x hg38.cpg_idx -m SRX012345.xsym.gz -o SRX012345.m16

If the chromosomes appear out-of-order in hg38.cpg_idx and SRX012345.xsym.gz an error will be reported.

If you begin with a counts format file, for example SRX012345.sym, created using the dnmtools counts and then dnmtools sym commands, then you will need to first convert it into .xsym format. You can do this as follows:

dnmtools xcounts -z -o SRX012345.xsym.gz -c hg38.fa -v SRX012345.sym

Once again, be sure to always use the same hg38.fa file. Strictly, what matters for the hg38.fa, or any other reference genome, is that the order and lengths or chromosomes are identical.

This step is to make sure everything is sensible. You will need a set of genomic intervals of interest. In this example these will be named intervals.bed. You also need the index file and the methylome file explained in the above steps.

mxe lookup local --log-level debug -x hg38.cpg_idx -m SRX012345.m16 -o intervals.bed.info -i intervals.bed

The index file hg38.cpg_idx and the methylome file SRX012345.m16 are the same as explained above. At the time of writing, the intervals.bed file must be 6-column bed format, so if yours is only 3 columns, you can use a simple awk command to pad it out as follows:

awk -v OFS="\t" '{print $1,$2,$3,"X",0,"+"}' intervals.bed3 > intervals.bed

The output in the intervals.bed.info file should be consistent with the information in the command:

dnmtools roi -o intervals.roi intervals.bed SRX012345.xsym.gz

The format of the output might be different, but the methylation levels on each line (i.e., for each interval) should be identical.

We will assume for now that the hostname of the remote mxe server is example.com, and the port is 5000 (the default). The following command should give identical output to the above command:

mxe lookup remote -s example.com -v debug -x hg38.cpg_idx -o intervals.bed.info -a SRX012345 -i intervals.bed

Note that now SRX012345 is not a file, but rather a methylome name, or accession, that is available on the server. If it is not, the server will respond that the accession is not available.