Question: trimming illumina single end DNA seq
gravatar for lnaren
2.9 years ago by
lnaren10 wrote:


I am trying to trim a single ended  DNAseq by using Trimmomatic tool. But "Input fastQ file" shows that "No fastqsanger dataset available". Same problem happened when I tried to use Map with bwa for Illumina tool as well.

I have uploaded the file into history. How can I complete the trimming and mapping?

Many thanks,


bwa galaxy • 917 views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by lnaren10
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Ren,

The input fastq dataset probably needs to have the "fastqsanger" datatype assigned.

These two wiki sections combined explain how to assign a datatype and equally important - how to make certain that datatype is correct. No one likes to start over - so I recommended first confirming the type, including making modificataions as needed, then executing the tools. If the data is a mismatch for assigned type, unexpected results can occur and not always with the first tool in the pipeline, which is always frustrating (for anyone doing bioinformatics, in Galaxy or through other means).


Support#Dataset_special_cases (section leads with fastq type testing plus how-to for manipulation if needed)

We hope this with your project! Jen, Galaxy team



ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
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