rmShortInserts {casper} | R Documentation

## Remove reads with short insert sizes from imported BAM files.

### 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.

[Package casper version 2.18.0 Index]