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Question: trimming my illumina sequences
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gravatar for c.torresi
20 months ago by
c.torresi • 0
c.torresi • 0 wrote:

Good morning, I am new in use of galaxy and I need help. I tried to trim my raw data from MiSeq using trim galore and trimmomatic but they generated empy files. where I was wrong? Then I used Trim sequences and I tried to open the output file by FASTQC to check it, but what i see is something strange, maybe I have to convert the output file from fastqsanger to fastq, if yes, who can I do it? thank you very much in advance

Claudia
trimming • 606 views
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modified 20 months ago by Mo Heydarian ♦ 830 • written 20 months ago by c.torresi • 0
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gravatar for Mo Heydarian
20 months ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello, Have you checked your data with FASTQC before trimming to ensure that your library contains reads with sufficient quality to pass the quality filters you set for the trimming tools used?

Also, please double check that your file format is "fastqsanger" and not one of the other "fastq*" formats that may not work correctly with the trimming tool. Nearly all of the tools in Galaxy that deal with Illumina reads require them to be in "fastqsanger" format.

If you are still having issues, please provide a sample of your reads here and maybe folks can give insight as to what is going on.

Hope this helps!

Cheers, Mo Heydarian
ADD COMMENT • link written 20 months ago by Mo Heydarian ♦ 830
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