Hey Jen,
I've already solved the cleaning problem using Seqclean.
Seqclean only takes fasta as input. So if you are dealing with fastq
files, you have to split them into quality and fasta, clean the fasta
file, trim the quality strings by yourself and put everything back
together ...
(If someone knows a better solution, plz tell me!)
It would be really cool if there was a Galaxy Tool that just takes fastq
and cleans it.
Thx,
Felix



> Hello Felix,
>
> The tools under "NGS: QC and manipulation -> Generic FASTQ manipulation"
> should be able to help, in particular "Manipulate FASTQ reads on various
> attributes" will allow you to enter a regular expression that could trim
> poly-A tails (the same way a perl script could, for example). The tool
> has link to more documentation about how to construct expressions). Or,
> if you know the length of the insert sequence you want to retain,
> "Filter FASTA" would be a good choice.
>
> Please give these a try and let us know if we can help more.
>
> Best!
>
> Jen
> Galaxy team
>
> On 2/23/11 4:34 AM, Felix Hammer wrote:
>> Hi,
>> is there a way to clean fastq files (filter Poly-A etc.) with Galaxy?
>> Haven't found anything so far. Also if you generally know good tools plz
>> answer.
>> Have seen lots of stuff for fasta and qual files but not for fastq.
>> Thx,
>> Felix
>>
>> _______________________________________________
>> The Galaxy User list should be used for the discussion
>> of Galaxy analysis and other features on the public
>> server at usegalaxy.org. For discussion of local Galaxy
>> instances and the Galaxy source code, please use the
>> Galaxy Development list:
>>
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other
>> Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org
>


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to