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Question: Cleaning Of Fastq Files
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gravatar for Felix Hammer
7.8 years ago by
Felix Hammer • 200
Felix Hammer • 200 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
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modified 7.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.8 years ago by Felix Hammer • 200
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gravatar for Jennifer Hillman Jackson
7.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 http://usegalaxy.org http://galaxyproject.org
ADD COMMENT • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k
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 REPLY • link written 7.7 years ago by Felix Hammer • 200
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? https://bitbucket.org/galaxy/galaxy- 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 http://usegalaxy.org http://galaxyproject.org
ADD REPLY • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k
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