rmShortInserts

 Object with aligned reads, as returned by <code>scanBam</code>  

 Reads with insert size smaller than <code>isizeMin</code> will be removed. 

isizeMin


  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 <code>calc</code>
  or <code>calcDenovo</code>.


 ~paired-end sequencing 

 ~SAM/BAM 

Infer alternative splicing from paired-end RNA-seq data.
The model is based on counting paths across exons, rather than
pairwise exon connections, and estimates the fragment size and
start distributions non-parametrically, which improves
estimation precision.

David Rossell

casper

Characterization of Alternative Splicing based on Paired-End
Reads

rmShortInserts function

Object with aligned reads, as returned by <code>scanBam</code>

Reads with insert size smaller than <code>isizeMin</code> will be removed.

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 <code>calc</code>
  or <code>calcDenovo</code>.

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

Description

Usage

Arguments

Value

Examples