[Bioperl-l] building NGS pipeline

[Adam Witney]

On 28 Feb 2011, at 15:03, Chris Fields wrote:

> 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 

Thanks Sean, Chris,

the bowtie/tophat/cufflinks set of tools seem to work well. I have also come across myrna also but I am still getting that setup.

Thanks again

adam