[EMBOSS] Trimming illumina short reads based on quality
David Martin
d.m.a.martin at dundee.ac.uk
Tue Dec 1 16:16:21 UTC 2009
>>> 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
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