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‎docs/404.html‎

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window.path_to_searchindex_js = "searchindex-b1d0ec24.js";
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‎docs/advanced_usage.html‎

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@@ -2219,14 +2219,17 @@ <h2 id="extract-calls"><a class="header" href="#extract-calls">extract calls</a>
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<h2 id="extract-read-stats"><a class="header" href="#extract-read-stats">extract read-stats</a></h2>
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<pre><code class="language-text">Produce a table where modification counts are summarized on the read level. This
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table will have one record per valid read and count the number of modified and
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unmodified bases for each base moficiation requested
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unmodified bases for each base modification requested
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Usage: modkit extract read-stats [OPTIONS] &lt;IN_BAM&gt; &lt;OUT_PATH&gt;
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Arguments:
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&lt;IN_BAM&gt; Input modBAM. Can be a path to a file or "-"/"stdin" for standard
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input
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&lt;OUT_PATH&gt; Path to file for output, default will be to stdout
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&lt;IN_BAM&gt;
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Input modBAM. Can be a path to a file or "-"/"stdin" for standard
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input
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&lt;OUT_PATH&gt;
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Path to file for output, default will be to stdout
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Options:
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--filter-threshold &lt;FILTER_THRESHOLD&gt;
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default for all other bases with: --filter-threshold A:0.70
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--filter-threshold 0.9 will specify a threshold value of 0.70 for
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adenine and 0.9 for all other base modification calls
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--mod-thresholds &lt;MOD_THRESHOLDS&gt;
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Specify a passing threshold to use for a base modification,
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independent of the threshold for the primary sequence base or the
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default. For example, to set the pass threshold for 5hmC to 0.8 use
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`--mod-threshold h:0.8`. The pass threshold will still be estimated as
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usual and used for canonical cytosine and other modifications unless
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the `--filter-threshold` option is also passed
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--mod-codes &lt;MOD_CODES&gt;...
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Specify which modcodes to tabulate, should be
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&lt;primary_base&gt;:&lt;mod_code&gt;
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--queue-size &lt;QUEUE_SIZE&gt;
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Queue size, maximum number of reads to be held in memory waiting for
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records to be written [default: 10000]
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records to be written
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[default: 10000]
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--io-threads &lt;IO_THREADS&gt;
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[default: 4]
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-h, --help
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Print help
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Print help (see a summary with '-h')
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Logging Options:
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--log-filepath &lt;LOG_FILEPATH&gt; Path to file to write run log
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--log-filepath &lt;LOG_FILEPATH&gt;
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Path to file to write run log
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--suppress-progress
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Hide the progress bar
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</code></pre>
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<h2 id="motif-bed"><a class="header" href="#motif-bed">motif bed</a></h2>
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<pre><code class="language-text">Create BED file with all locations of a sequence motif. Example: modkit motif
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--io-threads &lt;IO_THREADS&gt;
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Number of threads to use when for decompression [default: 4]
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</code></pre>
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<h2 id="dmr-isoform"><a class="header" href="#dmr-isoform">dmr isoform</a></h2>
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<pre><code class="language-text">Use a transcriptome-aligned bedMethyl table and GTF file to compare methylation
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across gene transcript isoforms. Run analysis on the entire transcriptome or on
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a single gene. Optionally also make plots for single genes
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Usage: modkit dmr isoform [OPTIONS] --gtf &lt;GTF&gt; &lt;INPUT_BEDMETHYL&gt; &lt;OUTPUT_TABLE&gt;
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Arguments:
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&lt;INPUT_BEDMETHYL&gt;
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Input bedmethyl table. Expected to be bgzip-compressed and have a .tbi
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tabix index. This bedMethyl table must be generated from a
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transcriptome-aligned modBAM, NOT a genome-aligned modBAM. Expected
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that this table was generated by pileup with `--modified-bases`
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argument
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&lt;OUTPUT_TABLE&gt;
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Path to output BED file or '-' for standard output
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Options:
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--gtf &lt;GTF&gt;
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Path to GTF file to use for transcript models. May be compressed
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--min-valid-coverage &lt;MIN_VALID_COVERAGE&gt;
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Minimum valid coverage required to use an entry from a bedMethyl. See
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the help for pileup for the specification and description of valid
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coverage
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[default: 1]
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--single-code &lt;SINGLE_MODIFICATION_CODE&gt;
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Calculate differential methylation for this modification code in
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isolation. Unmodified and other modification counts will be combined
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--full
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Include per-modification combined proportions per position and
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per-isoform proportions in output. Adding this flag will make the
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output file substantially larger
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--log-filepath &lt;LOG_FILEPATH&gt;
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Path to optional debug log (recommended)
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-g, --gene-id &lt;GENE_ID&gt;
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Only process this Gene Id
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-n, --gene-name &lt;GENE_NAME&gt;
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Only process this Gene Name
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--suppress-progress
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Don't show the progress bar
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-t, --threads &lt;THREADS&gt;
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Number of concurrent processors to use. Only used when running on all
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genes
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[default: 4]
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--plot &lt;PLOT&gt;
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Generate an SVG plot displaying the methylation positions on each
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isoform (filtered by --min-score or --max-pval) and the common exons
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of the gene. Also displays negative log of the p-value of the DMR
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metric. See the online documentation for an example
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--marker-positions &lt;MARKER_POSITIONS&gt;...
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Comma-separated list of genomic positions to draw a vertical dotted
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line and a label
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--width &lt;WIDTH&gt;
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SVG width in px
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[default: 1600]
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--track-height &lt;TRACK_HEIGHT&gt;
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Height per transcript track in px
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[default: 26]
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--track-gap &lt;TRACK_GAP&gt;
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Gap between transcript tracks in px
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[default: 18]
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--left-margin &lt;LEFT_MARGIN&gt;
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Left margin in px
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[default: 220]
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--right-margin &lt;RIGHT_MARGIN&gt;
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Right margin in px
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[default: 40]
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--top-margin &lt;TOP_MARGIN&gt;
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Top margin in px
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[default: 210]
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--bottom-margin &lt;BOTTOM_MARGIN&gt;
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Bottom margin in px
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[default: 50]
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--intron-px &lt;INTRON_PX&gt;
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Length, in px, of the compressed intron segments
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[default: 24]
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--top-bar-height &lt;TOP_BAR_HEIGHT&gt;
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Height in px of the top bar
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[default: 90]
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--min-score &lt;MIN_SCORE&gt;
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Only plot methylation markers with negative log p-value greater than
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this value
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--max-pval &lt;MAX_PVAL&gt;
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Only plot methylation markers with p-value less than this value
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-h, --help
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Print help (see a summary with '-h')
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</code></pre>
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<h2 id="dmr-compare-tx-sites"><a class="header" href="#dmr-compare-tx-sites">dmr compare-tx-sites</a></h2>
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<pre><code class="language-text">Uses two transcriptome-aligned bedmMethyl tables to compare methylation for two
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conditions at transcriptome sites aggregated at the gene level. This command
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will combine the methylation counts across isoforms into a single summary
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statistic per-site for the gene, then compare those counts between conditions at
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the gene level and report results on genomic coordinates. The transcript models
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are provided by a GTF file. Optionally make a volcano plot of the top-k
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differentially methylated sites per gene
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Usage: modkit dmr compare-tx-sites [OPTIONS] -a &lt;COND_A&gt; -b &lt;COND_B&gt; --out &lt;OUTPUT_TABLE&gt; --gtf &lt;GTF&gt;
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Options:
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-a &lt;COND_A&gt;
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Input bedmethyl table for first condition (condition 'A'). Expected to
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be bgzip-compressed and have a .tbi tabix index. This bedMethyl table
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must be generated from a transcriptome-aligned modBAM, NOT a
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genome-aligned modBAM. Expected that this table was generated by
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pileup with `--modified-bases` argument
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-b &lt;COND_B&gt;
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Input bedmethyl table for first condition (condition 'B')
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-o, --out &lt;OUTPUT_TABLE&gt;
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Path to output BED file or '-' for stdout
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--full
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Include combined proportions and counts for each condition. This will
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increase the size of the output file
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--gtf &lt;GTF&gt;
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Path to GTF file to use for transcript models. Can be compressed
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--min-valid-coverage &lt;MIN_VALID_COVERAGE&gt;
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Minimum valid coverage required to use an entry from a bedMethyl. See
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the help for pileup for the specification and description of valid
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coverage [default: 1]
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--single-code &lt;SINGLE_MODIFICATION_CODE&gt;
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Calculate differential methylation for this modification code in
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isolation. Unmodified and other modification counts will be combined
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--log-filepath &lt;LOG_FILEPATH&gt;
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Path to optional debug log (recommended)
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--suppress-progress
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Don't show the progress bar
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-t, --threads &lt;THREADS&gt;
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Number of concurrent processors to use [default: 4]
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--plot &lt;PLOT&gt;
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Path to file to create an SVG volcano plot where the x-axis is log2
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fold change and the y-axis is negative log p-value. See the online
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documentation for and example
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--top-k &lt;TOP_K&gt;
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For each gene, sort the positions in decreasing negative log p-value
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and take this many for plotting. Setting a large number will increase
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the size of the SVG plot [default: 1]
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--min-effect-size &lt;MIN_EFFECT_SIZE&gt;
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Discard positions with an effect size less than this before
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considering them for plotting [default: 0.1]
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--plot-title &lt;PLOT_TITLE&gt;
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Add a title to the plot
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--gene-labels &lt;GENE_LABELS&gt;
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Path to plain text file of a list of gene names, one per line, to mark
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in the volcano plot
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-h, --help
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Print help
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</code></pre>
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<h2 id="bedmethyl-merge"><a class="header" href="#bedmethyl-merge">bedmethyl merge</a></h2>
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<pre><code class="language-text">Perform an outer join on two or more bedMethyl files, summing their counts for
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records that overlap
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</code></pre>
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<h2 id="bedmethyl-map-to-genome"><a class="header" href="#bedmethyl-map-to-genome">bedmethyl map-to-genome</a></h2>
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<pre><code class="language-text">Map a transcriptome-aligned bedMethyl file to genome-coordinates based on a GTF
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Usage: modkit bedmethyl map-to-genome [OPTIONS] --transcript-id &lt;TRANSCRIPT_ID&gt; --gtf &lt;GTF&gt; &lt;INPUT_BEDMETHYL&gt; &lt;OUTPUT_BEDMETHYL&gt;
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Arguments:
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&lt;INPUT_BEDMETHYL&gt;
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&lt;OUTPUT_BEDMETHYL&gt;
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Options:
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-t, --transcript-id &lt;TRANSCRIPT_ID&gt;
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--transcript-version &lt;TRANSCRIPT_VERSION&gt;
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--gtf &lt;GTF&gt;
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--header
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-h, --help Print help
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</code></pre>
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<h2 id="modbam-adjust-mods"><a class="header" href="#modbam-adjust-mods">modbam adjust-mods</a></h2>
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<pre><code class="language-text">Performs various operations on BAM files containing base modification
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information, such as converting base modification codes and ignoring

‎docs/algo_details.html‎

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‎docs/collapse.html‎

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<nav class="nav-wrapper" aria-label="Page navigation">
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