WEP - Faq: WEP: Whole Exome Pipeline

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FAQ

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.

Analysis

  1. 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?
  3. Can I upload multiple files? And multiple samples?
  4. How long does a typical analysis take?

Archive

  1. What is a study? What's the difference with a project?

Results

  1. How can I quickly learn how to browse results?
  2. Is it possibile to download the results of my analysis?
  3. Where can I find additional documentation on the Results section?
  4. What is the Phred score?

Other

  1. I used the WEP tool for my project. How can I cite it?



Analysis

1. What input files are supported?
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.

[1] Warning: compressed archives obtained with Mac OS X require the windows-compatibility flag
2. How many samples can be uploaded and analyzed? How many analysis can be run? Are there any time limits?
An account with User rank can:
  • create up to 2 studies
  • upload up to 12 files
  • build up to 2 analyses
  • run 1 analysis at a time
3. Can I upload multiple files? And multiple samples?
Each sample has to be uploaded as a single file: you can upload multiple files if you have multiple samples.
The general rule is: 1 sample = 1 file, no merge operation will be executed by our system.
4. How long does a typical analysis take?
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.

Archive

1. 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.

Results

1. How can I quickly learn how to browse results?
Click on Results example (on the top navigation menu) to follow a guided tour of the results pages.
2. Is it possibile to download the results of my analysis?
Yes, you have two options:
  • Downloading the results directly from the analysis monitoring page.
  • From the Results page, after applying any filter, with the DOWNLOAD link.
Warning!
Data browsing and downloading has been optimized with caching/sessioning.
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.
3. Where can I find additional documentation on the Results section?
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 NGSrich and SAMtools. The explanation of the NGSrich statistics can be found in the presenting article.
4. What is the Phred score?
(from Wikipedia) 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 Wikipedia page.

Other

1. 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.
PMID 23815231

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