Question: How to visualize the data
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Jennifer Hillman Jackson ♦ 25k wrote:
Hello,
The image shared is not publically accessible. I am guessing that either no visualization options are available for the currently assigned datatype, the datatype is still non-specific (example: .txt) or that you do not know where to find them based on your other post (https://biostar.usegalaxy.org/p/23361/).
- First, assign the correct datatype to the dataset(s).
- Second, assign the correct database (genome build) to the dataset. This is needed for some options.
- After this, available visualization options will be in the "Visualize" menu within the expanded dataset. This menu is under the small graph icon.
This is what the graph icon looks like in the Galaxy interface: http://imgur.com/a/V6PP8
Help with formatting inputs is here: https://galaxyproject.org/support/#getting-inputs-right-
Certain tools also create data visualization graphics within Galaxy as the primary or optional output. Search by the datatype name in the tool panel to locate tools that generate the desired output type. If are looking for something specific and do not find it, let us know and we can help.
Thanks! Jen, Galaxy team
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mayurdoke • 10 wrote:
Hello,
Thank you for your reply. My data type is .txt and I have converted into fastaq format in Galaxy with FASTQ Groomer. After running the tool Fastqc, I could see my results about the data quality like [PASS]Basic Statistics Per base sequence quality, Per tile sequence quality, Per-sequence quality scores, Per base sequence content, Per-sequence GC content, Per base N content. But I could not see any graphs after clicking the graph icon in Galaxy interface. What is the reason behind that? Do I have to download any plugin for that? Thank you.
FastQC is one of those tools I mentioned that produces its own graphics. There are two outputs - one is a text report, one is a graphical report. Click on the "eye" icon for the dataset to view the graphical report in the center panel.
Guide for interpreting a FastQC report: https://galaxyproject.org/tutorials/ngs/#fastq-manipulation-and-quality-control
Fastq data itself will not have any graphics beyond what tools generate. Other types of output (BAM, GTF, other types of different tabular data) can be graphed using the "visualize" functions. These are usually statistics (can be general stats, the same as one would graph using other methods) or data that is descriptive of where features/summary data is located, often with respect to other features, against a reference transcriptome/exome/genome.
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Related question: https://biostar.usegalaxy.org/p/23361/