rmShortInserts {casper} | R Documentation |
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
.
rmShortInserts(bam, isizeMin=100)
bam |
Object with aligned reads, as returned by |
isizeMin |
Reads with insert size smaller than |
Named list, in the same format as that returned by scanBam
.
The insert size is stored in objects imported with scanBam
in the element named isize
.
David Rossell
##---- Should be DIRECTLY executable !! ---- ##-- ==> Define data, use random, ##-- or do help(data=index) for the standard data sets.