[Bioperl-l] Trimming low quality reads

[Chris Fields]

Ben,

I haven't used fastx directly, but from the docs I would guess fastx_clipper returns everything that isn't adaptor-only, has just N's, or is above a specified length.  (e.g. I would assume running 'fastx_clipper -k -n -l 0 <foo.fastq>' would return everything).  Is that not the case?

chris

On Feb 16, 2011, at 11:10 AM, Ben Bimber wrote:

> Fastx is great and we use those tools in a number of places, but If
> I'm not mistaken, doesnt its trimming involve filters their either
> including or excluding the read as a whole, rather than end clipping?
> 
> The need probably depends on your data.  With short reads, I could
> imagine that's what you want.  With 500bp 454 reads, end clipping is
> nice.  I ended up making a simple little (and not terribly efficient)
> script that does 3' end clipping.  My datasets are orders of magnitude
> smaller than what you posted though....
> 
> -Ben
> 
> 
> 
> 
> On Wed, Feb 16, 2011 at 10:59 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> +1 on using fastx.  I believe this is what our local seq pipeline uses prior to us sending out the processed stuff.
>> 
>> chris
>> 
>> On Feb 16, 2011, at 10:41 AM, Jason Stajich wrote:
>> 
>>> I would use a faster implementation like the fastx toolkit - http://hannonlab.cshl.edu/fastx_toolkit/
>>> 
>>> There are lots of answers to NGS questions on seqanswers too
>>> http://www.google.com/search?q=site:seqanswers.com+trim
>>> 
>>> 
>>> Jordi Durban wrote:
>>>> Well, there's a program called Seqtrim that uses bioperl to trim the
>>>> sequences.
>>>> Here more information:
>>>> http://www.scbi.uma.es/cgi-bin/seqtrim/seqtrim_login.cgi
>>>> Hope this helps.
>>>> 
>>>> 2011/2/16 shalabh sharma<shalabh.sharma7 at gmail.com>
>>>> 
>>>>> Hi,
>>>>>    Is there any bioperl module available to quality trim in fasta-qual
>>>>>  format.
>>>>> i am little worried about the efficiency as i have huge data (~ 50 gb).
>>>>> Also i would really appreciate if some one has some other suggestions.
>>>>> 
>>>>> Thanks
>>>>> Shalabh
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>>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> --
>>> Jason Stajich
>>> 
>>> 
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>> 
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