[Bioperl-l] Trimming low quality reads

[Ben Bimber]

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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