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docs/content/counts-nano.md

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+# counts-nano - compute single-site methylation from nanopore data
+
+## Synopsis
+```console
+$ dnmtools counts-nano [OPTIONS] -c <chroms> <input.bam>
+```
+
+## Description
+
+The `counts-nano` command introduced in v1.5.0 is designed specifically to
+generate DNMTools [counts](../counts) format files from nanopore data called
+for the `5mCG_5hmCG` modification. Currently this is only supported for
+methylation and hydroxymethylation called at CpG sites.
+
+More documentation will come as this tool evolves, but for now:
+
+- Most behavior is very similar to what you will find from [counts](../counts).
+- Mutation information is not estimated by `nano-counts`.
+- Currently this only works for CpG sites and when the only modified sites are
+  marked as `C+m?` or `C+h?` in the `MM` field of each BAM/SAM read record.
+- The first 6 columns of the output are the same as explained in the
+  [counts](../counts) format, except the fraction for the 5th column is both
+  5mC and 5hmC. The 7th column is for 5hmC alone and the 8th is for 5mC alone.
+- The methylation levels will not result in integer values when multiplied by
+  the number of reads because probabilities on modifications are used, so
+  methylation levels for each site are expected values (the best estimates we
+  can make), and do not use arbitrary cutoffs.
+- Other commands in DNMTools have been modified to use this form of expected
+  methylation level, and behave as previously for bisulfite sequencing data,
+  but have updated behavior when the data is from nanopore. The user does not
+  need to specify the technology used.
+- Some commands need to use a `-relaxed` flag to work with the additional
+  columns in the output from `counts-nano` compared with `counts`. For
+  commands without this option, simply do `cut -f1-6` on the output of
+  `counts-nano` to remove those.
+
+## Options
+
+```txt
+-o, -output
+```
+Output file name. The default is to write output to the terminal,
+which is not useful unless commands are piped.
+
+```txt
+-c, -chrom
+```
+Reference genome file, which must be in FASTA format. This is
+required.
+
+```txt
+-t, -threads
+```
+
+The number of threads to use. This is only really helpful if the input is BAM
+(not helpful for SAM), and the output is to be zipped (see `-z` below). These
+threads are used to decompress BAM input and compress gzip output. If only one
+of these conditions holds, using more threads can still help. Because most
+computation in `counts-nano` is processing reads sequentially, using too many
+threads will have decreasing returns.
+
+```txt
+-z, -zip
+```
+
+The output should be zipped (in gzip format). This is not deduced by the
+filename, but specifying this argument should be accompanied by using a `.gz`
+filename suffix for the output.
+
+```txt
+-n, -cpg-only
+```
+
+Print only CpG context cytosines. This significantly reduces the output size
+in most genomes. Note that using this option does not merge data as symmetric
+CpGs.
+
+```txt
+-sym
+```
+
+This will turn on `-n, -cpg-only` automatically and will output symmetric CpG
+sites, with each level including all counts and methylation levels as a
+(weighted) average of both strands.
+
+```txt
+-H, -header
+```
+
+Add a header to the output file to identify the reference genome. This will be
+in the form of "comment" lines beginning with `#`. This is not required for most
+downstream processing, but is used by commands that check for consistency with
+a reference genome.
+
+```txt
+-v, -verbose
+```
+
+Report more information while the program is running.
+
+```txt
+-progress
+```
+Show progress while the program is running.