[Bioperl-l] Trimming low quality reads

[Ben Bimber]

hi chris,

you're right on fastx_clipped, but i think the tool i'm remembering is
called quality filter or something.  it does things like filter reads
containing Ns, reads with total quality below a threshold etc.

as the same suggests, it removes low qual reads, but does not appear
to trim per se.

-ben



On Wed, Feb 16, 2011 at 11:49 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 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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