rmShortInserts: Remove reads with short insert sizes from imported BAM files.

In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description

In paired-end experiments short inserts (i.e. the 2 ends being very close to each other), may indicate RNA degradation or that a short RNA (e.g. miRNA) is being sequenced. Typically the goal is not to study alternative splicing for such short/degraded RNA; in this case it is recommendable to remove such short inserts to avoid biasing the insert size distribution. Requiring a minimum insert size can also result in significantly faster computations when quantifying alternative splicing via calc or calcDenovo.

Usage

rmShortInserts(bam, isizeMin=100)

Arguments

bam	Object with aligned reads, as returned by scanBam
isizeMin	Reads with insert size smaller than isizeMin will be removed.

Value

Named list, in the same format as that returned by scanBam.

Note

The insert size is stored in objects imported with scanBam in the element named isize.

Author(s)

David Rossell

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

casper documentation built on Dec. 17, 2020, 2:01 a.m.