[EMBOSS] Trimming illumina short reads based on quality

[David Martin]

>>> On 12/1/2009 at  3:46 PM, in message <4B153A4C.6000904 at umdnj.edu>, Ryan Golhar <golharam at umdnj.edu> wrote:
I think virtually every man and his dog who has done anything with Illumina reads has a variety of perl scripts that do this. It depends how you want to do the trimming. Do you want to clip to a specific length, clip on quality (absolute or average over a window) and do you have a minimum length requirement? 

Do you want to clip 3' and 5' ends or just one? 

..d 


Michael,

Doesn't Illumina provide tools to do this?  I know with ABI Solid data,
they have a perl script capable of trimming data based on quality scores.

Ryan


michael watson (IAH-C) wrote:
> Hi
>
> I'm sorry if I've not been keeping up to date on what is doubtless a hot topic.
>
> Does EMBOSS allow one to trim short reads based on quality data (from a fastq file)?
>
> If not, I have read that it is planned - any idea when it will be implemented?
>
> Otherwise, alternative suggestions are welcome!
> 



David Martin PhD
College of Life Sciences
University of Dundee 
The University of Dundee is a Scottish Registered Charity, No. SC015096.


The University of Dundee is a registered Scottish charity, No: SC015096