generates a coverage bigWig file from a given BAM or CRAM filebamCoveragedeepTools_macros.xml
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.. image:: $PATH_TO_IMAGES/bamCoverage_output.png
:width: 600
:height: 450
Usage hints
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* A smaller ``bin size`` value will result in a higher resolution of the coverage track but also in a larger file size.
* The ``1x normalization`` (RPGC) requires the input of a value for the **effective genome size**, which is the mappable part of the reference genome. Of course, this value is species-specific.
* It might be useful for some studies to exclude certain chromosomes in order to avoid biases, e.g. chromosome X for many mammals where the males contain a pair of each autosome, but often only a single X chromosome.
* By default, the read length is **NOT** extended! This is the preferred setting for **spliced-read** data like RNA-seq, where one usually wants to rely on the detected read locations only. A read extension would neglect potential splice sites in the unmapped part of the fragment.
Other data, e.g. ChIP-seq, where fragments are known to map contiuously, should be processed with read extension (``--extendReads [INT]``).
* For paired-end data, the fragment length is generally defined by the two read mates. The user-provided fragment length is only used as a fallback for singletons or mate reads that map too far apart (with a distance greater than four times the fragment length or if the mates are located on different chromosomes).
WARNING: If you already normalized for GC bias using ``correctGCbias``, you should absolutely **NOT** set the parameter ``--ignoreDuplicates``!
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@REFERENCES@
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