On Sat, May 9, 2009 at 7:14 AM, Wu, Xiwei <XWu@coh.org> wrote:

> Dear all,
>
> I have been working on a small RNA sequencing data set. After adapter
> trimming, the length of each tag is different, ranging from 16 to 40.
> While I am using pileup function in SHortRead package to calculate the
> coverage, it only allows a uniform length of tags, which will generate
> inaccurate coverage. Is it possible to set different tag length, or any
> other functions allowing this in other packages? Thanks in advance.
>

I think the fraglength parameter can be a vector, so yes you can specify a
length for each tag.

There's always coverage() in IRanges which sounds similar to pileup() and
probably uses less memory through run-length encoding.

Michael


> Xiwei Wu
> City of Hope
>
>
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