Megalodon_Output_Notes.txt

Megalodon Modified Basecalling Output Notes:

made from:
https://nanoporetech.github.io/megalodon/file_formats.html
https://nanoporetech.github.io/megalodon/common_arguments.html
https://nanoporetech.github.io/megalodon/advanced_arguments.html
For BedMethyl: https://www.encodeproject.org/data-standards/wgbs/
Looking at actual output

Output options passed to Megalodon:
basecalls mod_basecalls mappings mod_mappings per_read_mods mods

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basecalls: Canonical, produces FASTQ with first line ONLY containing the read_id (no runid, sampled, read, ch or start_time).

Files: basecalls.fastq 
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mod_basecalls: produces HDF5 file with a data set corresponding to each read (accessed via the read_id)

Files: basecalls.modified_base_scores.hdf5
--

--
mappings: Mapped reads will be output into a SAM, BAM (default) or CRAM file. A mapping summary (mappings.summary.txt) will also be produced, containing the following fields read_id pct_identity num_align       num_match num_del num_ins read_pct_coverage chrom strand  start end.

Files:mappings.bam, mappings.summary.txt
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--
mod_mappings: provide reference-anchored per-read modified base calls.
These mappings contain the mapped reference sequence annotated with modified base calls. Useful for visualizing per-read modified base calls (e.g. IGV bisulfite mode for CpG calls)

Files: mod_mappings.5mC.bam, mod_mappings.6mA.bam (both are produced even if a specific motif is requested)
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per_read_mods (Per-read Modified Bases): 
Tab-delimited (instead of SQLite output, with flag --write-mods-text)
Contains the following fields: read_id, chrm, strand, pos, mod_log_prob, can_log_prob, mod_base, motif

Files: per_read_modified_base_calls.db, per_read_modified_base_calls.txt
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mods:
Aggregated Modified Bases: bedmethyl format with one file per modification type. Produced at the end of the run, I/O intensive.

Each column represents the following:

    Reference chromosome or scaffold
    Start position in chromosome
    End position in chromosome
    Name of item
    Score from 0-1000. Capped number of reads
    Strandedness, plus (+), minus (-), or unknown (.)
    Start of where display should be thick (start codon)
    End of where display should be thick (stop codon)
    Color value (RGB)
    Coverage, or number of reads
    Percentage of reads that show methylation at this position in the genome

Files: modified_bases.5mC.bed, modified_bases.6mA.bed (both are produced even if a specific motif is requested)

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