[Bioperl-l] building NGS pipeline

[Chris Fields]

On Feb 28, 2011, at 6:04 AM, Sean Davis wrote:

> 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

BioPerl does have wrappers and interfaces for some packages, particularly Lincoln's Bio::DB::Sam (samtools package) and wrappers for bowtie, tophat, and bwa.  Locally, for comparative gene expression analyses we use bioconductor (many packages to choose from) as well as the command-line tools Sean mentions.

chris