Frequently asked questions
We warmly invite you to read our Help
section too. If you still have some doubts about our tool, please write us from our feedback page
- What input files are supported?
- How many samples can be uploaded and analyzed? How many analysis can be run? Are there any time limits?
- Can I upload multiple files? And multiple samples?
- How long does a typical analysis take?
- What is a study? What's the difference with a project?
- How can I quickly learn how to browse results?
- Is it possibile to download the results of my analysis?
- Where can I find additional documentation on the Results section?
- What is the Phred score?
- I used the WEP tool for my project. How can I cite it?
Analysis1. What input files are supported?
2. How many samples can be uploaded and analyzed? How many analysis can be run? Are there any time limits?
The WEP tool supports:
- short-read data-sets produced by Illumina sequencing platforms (FASTQ)
- several standard file formats (SRA, BAM)
- compressed archives (zip1, tar, gzip, bz or bz2 compression are admitted)
WEP automatically detects the type of uploaded file and chooses the necessary program to decompress it.
 Warning: compressed archives obtained with Mac OS X require the windows-compatibility flag
3. Can I upload multiple files? And multiple samples?
An account with User
- create up to 2 studies
- upload up to 12 files
- build up to 2 analyses
- run 1 analysis at a time
Each sample has to be uploaded as a single file: you can upload multiple files if you have multiple samples.4. How long does a typical analysis take?
The general rule is: 1 sample = 1 file, no merge operation will be executed by our system.
The amount of time required by an analysis execution is influenced by different factors, such as:
- The amount of files uploaded
- The sequencing region (genome-wide or targeted)
- The number of jobs waiting for execution on our servers
However, you can find an estimated execution time in your analysis monitoring page.
Archive1. What is a study? What's the difference with a project?
According to the EBI/ENA data format standard, a study contains information about the a single sequencing project (more analysis can be run in a single study). So, in practice, a study contains all the information about a project.
Results1. How can I quickly learn how to browse results?
2. Is it possibile to download the results of my analysis?
Click on Results example
(on the top navigation menu) to follow a guided tour of the results pages.
3. Where can I find additional documentation on the Results section?
Yes, you have two options:
Data browsing and downloading has been optimized with caching/sessioning.
- Downloading the results directly from the analysis monitoring page.
- From the Results page, after applying any filter, with the
While this ensures better performance in page loading,
as a drawback opening different tabs on different samples may lead to data misconfiguration.
Please ensure to filter and download one sample at the time.
4. What is the Phred score?
Most of the explanations about the variant calling algorithm can be found in the help section of the GATK project
If you need further details about the annotation step, please refer to the ANNOVAR website
In the Statistics
tab of the Results page, you'll find a statistical overview produced by
The explanation of the NGSrich statistics can be found in the presenting article
Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities.
The Phred score is the most common measure of base calling quality. For further information detail, you can refer to the
Other1. I used the WEP tool for my project. How can I cite it?
BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.
WEP: a high-performance analysis pipeline for whole-exome data.
D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.
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