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
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