| | Report the depth at each genome position with 1-based coordinates.
**Output format:** `chromosome position depth`
**Default behavior:** Reports coverage histogram instead
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| | Report depth at each genome position with 0-based coordinates.
**Features:**
- Only reports positions with non-zero coverage
- Uses 0-based coordinate system
- More memory efficient than `--depth`
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| | Report depth in BedGraph format for genome browser visualization.
**Output format:** `chromosome start end depth`
See [BedGraph specification](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) for details.
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--bed_graph_zero_coverage -bga | | Report depth in BedGraph format including zero-coverage regions.
**Features:**
- Same as `--bed_graph` but includes regions with 0 coverage
- Useful for finding uncovered regions: `grep -w 0$ output.bg`
- Generates larger output files
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| | Treat "split" BAM or BED12 entries as distinct BED intervals.
when computing coverage.
For BAM files, this uses the CIGAR "N" and "D" operations
to infer the blocks for computing coverage.
For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds
fields (i.e., columns 10,11,12).
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--ignore_deletion -ignoreD | | Ignore local deletions (CIGAR "D" operations) in BAM entries
when computing coverage.
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| | Calculate coverage of intervals from a specific strand.
With BED files, requires at least 6 columns (strand is column 6).
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| | Calculate coverage of pair-end fragments.
Works for BAM files only
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| | Force to use provided fragment size instead of read length
Works for BAM files only
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| | Change strand af the mate read (so both reads from the same strand) useful for strand specific
Works for BAM files only
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| | Calculate coverage of 5" positions (instead of entire interval).
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| | Calculate coverage of 3" positions (instead of entire interval).
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| | Combine all positions with a depth >= max into
a single bin in the histogram. Irrelevant
for -d and -bedGraph
- (INTEGER)
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| | Scale the coverage by a constant factor.
Each coverage value is multiplied by this factor before being reported.
Useful for normalizing coverage by, e.g., reads per million (RPM).
- Default is 1.0; i.e., unscaled.
- (FLOAT)
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| | Adds a UCSC/Genome-Browser track line definition in the first line of the output.
- See here for more details about track line definition:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html
- NOTE: When adding a trackline definition, the output BedGraph can be easily
uploaded to the Genome Browser as a custom track,
BUT CAN NOT be converted into a BigWig file (w/o removing the first line).
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| | Writes additional track line definition parameters in the first line.
- Example:
-trackopts 'name="My Track" visibility=2 color=255,30,30'
Note the use of single-quotes if you have spaces in your parameters.
- (TEXT)
|