Question: Cleaning Of Fastq Files
gravatar for Felix Hammer
7.8 years ago by
Felix Hammer200
Felix Hammer200 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
galaxy • 1.4k views
ADD COMMENTlink modified 7.7 years ago by Jennifer Hillman Jackson25k • written 7.8 years ago by Felix Hammer200
gravatar for Jennifer Hillman Jackson
7.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson
ADD COMMENTlink written 7.7 years ago by Jennifer Hillman Jackson25k
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
ADD REPLYlink written 7.7 years ago by Felix Hammer200
Felix, Great that you solved the issue, we appreciate your letting us know! Would you like to open a request at bitbucket for adding in the tool? central/issues?status=new&status=open Or, I can open a ticket if you would like, just let me know. (Apologies if you already opened one, I searched and didn't find a ticket for this). Thanks! Jen -- Jennifer Jackson
ADD REPLYlink written 7.7 years ago by Jennifer Hillman Jackson25k
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