coverage.targetlength.plot
(Package: TEQC) :
Number of reads or average coverage versus target length scatter plot
Plots either numbers of on-target reads or average per-target coverage (or potentially other per-target values) against respective target lengths. A smoothing spline is added to the scatter plot.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: coverage.targetlength.plot
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2 images
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Visualization of target coverage uniformity. A line shows the cumulative fraction of targeted bases that reach at least a certain normalized coverage.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: coverage.uniformity
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1 images
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covered.k
(Package: TEQC) :
Target capture sensitivity
Calculates fraction of target bases covered by at least k reads
● Data Source:
BioConductor
● Keywords: math
● Alias: covered.k
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0 images
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Barplot showing fractions of reads / read pairs which are unique and for which there are two, three, ... copies. Separate bars are made for on- and off-target reads / read pairs
● Data Source:
BioConductor
● Keywords: hplot
● Alias: duplicates.barplot
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2 images
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Calculates the fraction of reads that align to target regions. Can also be used to retrieve those reads mapping to targets.
● Data Source:
BioConductor
● Keywords: math
● Alias: fraction.reads.target
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0 images
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fraction.target
(Package: TEQC) :
Fraction of the target within the genome
Calculates the fraction of the reference genome that is targeted
● Data Source:
BioConductor
● Keywords: math
● Alias: fraction.target
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0 images
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get.baits
(Package: TEQC) :
Read capture hybridization probe positions
Reads a file containing positions and sequences of the capture hybridization probes and creates a RangedData object.
● Data Source:
BioConductor
● Keywords: file
● Alias: get.baits
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0 images
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get.reads
(Package: TEQC) :
Read genomic positions of sequencing data
Reads a bedfile containing positions of sequenced read aligned to a reference genome and creates a RangedData object.
● Data Source:
BioConductor
● Keywords: file
● Alias: get.reads
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0 images
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get.targets
(Package: TEQC) :
Read capture target positions
Reads a bedfile containing positions of the capture targets and creates a RangedData object.
● Data Source:
BioConductor
● Keywords: file
● Alias: get.targets
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0 images
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Computes read pair insert sizes, i.e. distance from first base of first read to last base of second read of a read pair, and plots a histogram for all insert sizes.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: insert.size.hist
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1 images
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