CottonGen FAQ

FAQ Outline

About CottonGen

  1. What is CottonGen?
  2. What data and information does CottonGen contain?
  3. How is CottonGen supported?
  4. How is CottonGen structured?
  5. How do I cite CottonGen?
  6. How can I contact CottonGen?

Data Curation, Submission and Download

  1. Can I submit my data to CottonGen?
  2. Can I download data from CottonGen?
  3. Who should I contact if I think I have found a mistake in the database?
  4. Who contributes data and/or assistance to CottonGen?
  5. How can I find what’s new in CottonGen?
  6. How do I know what’s coming next in CottonGen

CottonGen Data

  1. Do I need a CottonGen account to access data?
  2. What types of markers does CottonGen house? 
  3. Is there a tutorial or help section on how to find marker information?
  4. What types of maps does CottonGen house?
  5. Can I view a list of all the maps with detailed information, such as genome, population size, etc?
  6. Is there a tutorial or help section on how to use the comparative map (CMap) viewer?
  7. Is there a tutorial or help section on how to use the Genome Browser (GBrowse) viewer?
  8. What genome data is available on CottonGen GBrowse?

CottonGen BIMS (Breeding Information Management System)

  1. What is BIMS?
  2. How do I use BIMS?
  3. BIMS FAQ

 

  About CottonGen

  • What is CottonGen?
CottonGen is a cotton community genomics, genetics and breeding database for facilitating basic, translational and applied research in cotton.  It is built using the open-source Tripal database infrastructure.  CottonGen consolidates and expands the data from CottonDB and the Cotton Marker Database, providing enhanced tools for easy querying, visualization and downloading of research data.
  •  What data and information does CottonGen contain?
The current major data components of CottonGen are:
More information on searching these data types can be found in the CottonGen User Manual: Data Searches.  For details on data numbers, please see the Data Overview Page.
  •  How is CottonGen Supported?
The CottonGen project is funded by:
  •  How is CottonGen structured?
CottonGen uses Tripal, a toolkit for construction of online genomic and genetic databases.  Tripal provides a web-front end for the Generic Database schema Chado which houses biological data. Tripal also integrates with Drupal, a Content Management System (CMS) that enables non-technical users to provide content, provides user management and social capabilities, and provides site developers with an interface that facilitates easier construction of websites.
  •  How do I cite CottonGen?
If you use CottonGen data or tools in your research, please use the following citation to reference us (not the database URL):
Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy R, Main D (2014) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research 42(D1), D1229-D1236.
 
To cite original data sources, look for the "Publication" link in the left-hand menu of CottonGen feature pages.
  • How can I contact CottonGen?
    The CottonGen staff can be reached via this contact form, or by selecting "Contact Us" under Help in the header menu.

(back to top)

 

Data Curation, Submission and Download

  • Can I submit my data to CottonGen?
We accept data that is peer reviewed via manuscript submission.  Data submission templates are available for uploading map, marker and germplasm evaluation data. If you have any questions please contact us using this contact form and we will work with you to input your data.  If you have expression or genomic data, please contact us before attempting to submit.
  • Can I download data from CottonGen?
Yes.  There are different ways to download data from CottonGen:
  • Via the Download page for genome annotations and other large static bulk data sets
  • Via the MainLab FTP repository
  • CottonGen chado data can be downloaded through CottonGen-related search pages.  After completing a search you have the option to download the matching data (refer to the CottonGen User Manual: Data Searches for details).
  • CottonGen CMap data can be downloaded via the CMap Map Set Info page
  • CottonGen genome alignment data and sequences under a specific chromosome and region can be downloaded via CottonGen JBrowse (refer to this JBrowse video tutorial for details). 
  • Who should I contact if I think I have found a mistake in the database?
Please contact us via this contact form, or by selecting "Contact Us" under Help in the header menu.
  • Who contributes data and/or assistance to CottonGen?
CottonGen has several collaborators and many contributors. See our Data Contributor page for details.  If you are looking for a specific individual, you can search using their name here.
  • How can I find what’s new in CottonGen?
You can find what has recently been accomplished on the Work Completed page, found under General in the header menu.
  • How do I know what’s coming next in CottonGen?
You can find work in progress at CottonGen through the Work in Progress page, found under General in the header menu.

(back to top)

CottonGen Data

  • Do I need a CottonGen account to access data?
No, you do not need an account to view publicly available data.  CottonGen also houses private breeding data for which breeders need an account to access and transfer.
  • What types of markers does CottonGen house?
CottonGen currently contains data on the following marker types:
  • Amplified fragment length polymorphism (AFLP)
  • Bacterial artificial chromosome end sequences (BAC-end)
  • Cleaved amplified polymorphic sequences (CAPS)
  • Diversity Arrays Technology Markers (DArT)
  • Exon targeted intron-exon splice junction (ET-ISJ)
  • Intron targeted intron-exon splice junction (IT-ISJ)
  • Insertion or deletion of bases (InDel)
  • Isoenzyme
  • Morphological markers
  • Restriction site associated DNA markers (RAD)
  • Random amplification of polymorphic DNA (RAPD)
  • Retrotransposon-microsatellite amplified polymorphism (REMAP)
  • Restriction fragment length polymorphism (RFLP)
  • Resistance gene analog polymorphism (RGAP)
  • Reverse transcription (RT)
  • Quantitative reverse transcription PCR (RT-qPCR)
  • Single-nucleotide polymorphism (SNP)
  • Sequence related amplified polymorphism (SRAP)
  • Simple sequence repeat (SSR)
  • Sequence-tagged site (STS)
  • Target region amplification polymorphism (TRAP)
The majority of markers in this database are SNP and SSR.  All of the above marker types are searchable from the CottonGen Marker Search.  View the Data Overview page for the number of each marker type.
  • Is there a tutorial or help section on how to find marker information?
Yes.  Please see the CottonGen User Manual: Markers.
  • What types of maps does CottonGen house?
CottonGen currently has over 80 maps total, including genetic (many with QTLs), bin, consensus, and in silico maps. These can be viewed through the Map Data Summary page.
  • Can I view a list of all the maps with detailed information, such as genome, population size, etc?
The complete list of maps available on CottonGen, including map details, is available on the Map Data Summary page.
  • Is there a tutorial or help section on how to use the map viewer(s)?
Yes.  Map Viewer User Manual shows how to use CottonGen Map Viewer and CMap User Tutorial shows how to use Comparative Map (CMap)
  • Is there a tutorial or help section on how to use JBrowse?
Yes. Please see this JBrowse video tutorial.
  • What genome data is available on CottonGen JBrowse?
The following genome assemblies are available on CottonGen JBrowse :
  • Gossypium arboreum A2 genome CGP-BGI assembly v2.0 (annotation v1.0)
  • Gossypium barbadense AD2 genome HAU-SGI assembly v1.0 (annotation v1.0)
  • Gossypium hirsutum AD1 genome Tx-JGI assebly v1.1
  • Gossypium hirsutum AD1 genome CGP-BGI assembly v1.0 (annotation v1.0)
  • Gossypium hirsutum AD1 genome NAU-NBI assembly v1.1 (annotation v1.0)
  • Gossypium raimondii D5 genome JGI assembly v2.0 (annotation v2.1)
  • Gossypium raimondii D5 genome CGP-BGI assembly v1.0
  • Gossypium arboreum  chloroplast (A genome)
  • Gossypium barbadense chloroplast (AD genome)
  • Gossypium hirsutum chloroplast (AD genome)
  • Gossypium raimondii chloroplast  (D genome)

(back to top)

Breeding Information Management System (BIMS)

  • What is BIMS?
CottonGen BIMS (Breeding Information Management System) is a Tripal module being developed by Mainlab Bioinformatics which allows users to explore the publically available breeding data in CottonGen while also providing a data management solution for private breeding programs.
  • How do I use BIMS?
The BIMS user manual is available here.

(back to top)