countFragmentOverlapsSecondCutter

object

Defines whether the read start should be extended by the length
of the second cutter recognition sequence to overlap the cutting sites which is
required for counting. If the cutting site has been trimmed with the primer
sequence this has to be set to <code>TRUE</code>. Default is <code>TRUE</code>.

extend

Minimum mapping quality required for counting the read.
Default is <code>0</code>. If set to negative values the filtering step is skipped.

minMapq

Maximum difference in starts or ends between read and fragment
positions. Default is <code>0</code>.

shift


<code>countFragmentOverlapsSecondCutter</code> counts the number of reads mapping to
each cutting site of the second cutter and then summarizes them over the
fragment ends of the first cutter stored in <code>rowRanges</code> of the
<code>FourC</code> object.


FourCSeq is an R package dedicated to the analysis of
(multiplexed) 4C sequencing data. The package provides a
pipeline to detect specific interactions between DNA elements
and identify differential interactions between conditions. The
statistical analysis in R starts with individual bam files for
each sample as inputs. To obtain these files, the package
contains a python script (extdata/python/demultiplex.py) to
demultiplex libraries and trim off primer sequences. With a
standard alignment software the required bam files can be then
be generated.

Felix A Klein

FourCSeq

Package analyse 4C sequencing data

countFragmentOverlapsSecondCutter function

<code>countFragmentOverlapsSecondCutter</code> counts the number of reads mapping to
each cutting site of the second cutter and then summarizes them over the
fragment ends of the first cutter stored in <code>rowRanges</code> of the
<code>FourC</code> object.

countFragmentOverlapsSecondCutter: Count fragment overlaps when sequencing was performed from the second cutting site

Description

Usage

Arguments

Value

See Also

Examples