[Bioc-sig-seq] pileup() for small RNA sequencing

[Simon Anders]

Dear Xiwei Wu

> 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.

The two parameters that control length, namely 'fraglength' and
'readlength' both take either a scalar or a vector. If you pass a scalar
this value is used for all reads, and if you pass a vector, you can
specify a different length for each read. The vector must, of course, have
as many elements as there are reads.

In the simplest case, pass a vector with the tag lengths for all the reads
as "fraglength" and leave "readlength" empty. Then, the same vector is
used for both parameters. If you havea fixed fragement length, you can
pass this as a single scalar and pass your vector of tag lengths as
"readlength". (For more information on the difference between these two,
see the vignette on ShortRead and HilbertVis.)

HTH
  Simon