[Bioperl-l] building NGS pipeline

[Sean Davis]

On Mon, Feb 28, 2011 at 6:06 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> Hi,
>
> I'm trying to put together a set of steps to runs some analysis on NGS data
> we have. I have found modules that wrap alignment software such as
> bowtie/bwa/maq, but are there any packages to calculate RPKM's etc? what are
> people using for this?
>
>
scripture, cufflinks/cuffdiff, bioconductor (GenomicFeatures package, for
example), ERANGE (wold lab), and several others.  I don't know of perl
wrappers for these, but they are all command-line applications, generally
speaking.

This is an interesting site to follow for RNA-seq analysis and applications:

http://rna-seqblog.com/

Sean