Frequently Asked Questions

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Question:
What is SCNBase?
Answer:

SCNBase is a website designed as a centralized knowledge base for SCN researchers and producers.  It contains genomics, genetics, population data along tools to translate this information in to practical applications.  SCNBase uses...

Question:
Who supports SCNBase.org?
Answer:

SCNBase is currently supported by the North Central Soybean Research Program, as part of a larger effort to enhance durability of SCN resistance for long-term, strategic SCN management. 

Question:
How can I convert my bam file to a bigwig file, and make it publicly available on JBrowse?
Answer:

There are at least 4 programs/scripts that are needed to convert a bam to a bigwig file from a standard read mapping bam file. 2 of these are non-standard and will probably need to be downloaded, but are very simple to use and install.

#...

Question:
How do I upload a vcf file to make it publicly viewable on scnbase.org?
Answer:

Tabix is a program that is necessary to be able to index the vcf file for upload and display in Jbrowse.  Once this program is installed, the process is fairly easy.

Be aware that your scaffold names must match the Jbrowse scaffold...

Question:
How do I get a bam file uploaded to SCNbase.org and have it publicly viewable in Jbrowse?
Answer:

First thing to consider, is your bam file larger than 10Gb?  10Gb is the maximum allowable file size to upload to SCNbase, and thus you will not be able to make it publicly available.  However, files that are larger than 10Gb can be...

Question:
With thousands of formats possible in a gff, what is the easiest method to upload a gff file that is viewable in Jbrowse?
Answer:

Tabix is a program that is necessary to be able to index the gff file for upload and display in Jbrowse.  However, getting a gff file viewable in jbrowse is a little more work than a bed file. 

1. Sort your gff file by scaffold...

Question:
With all of the possible formats to a bed file, what is the easiest mechanism to upload a bed file that is viewable in Jbrowse?
Answer:

Tabix is a program that is necessary to be able to index the bed file for upload and display in Jbrowse.  Once this program is installed, the process is fairly easy.

1. Sort your bed file by scaffold name and position.  Typically...

Question:
How do I cite SCNBase.org?
Answer:

Masonbrink, Rick E., Arun Seetharam, Usha Muppirala, Matthew Hudson, Melissa Mitchum, Thomas Baum, and Andrew Severin. "SCNBase." SCNBase. North Central Soybean Research Program, 8 Dec. 2016. Web. 12 Dec. 2016.

Question:
What is a SCNBase data curator?
Answer:

A data curator has expertise in bioinformatics or experience with GMOD tools and JBrowse.  The fastest way to get your data loaded into SCNBase is for a member of each group to familiarize themselves with standard file upload forms. ...

Question:
Who supports SCNBase.org?
Answer:

SCNBase is currently supported by the North Central Soybean Research Program, as part of a larger effort to enhance durability of SCN resistance for long-term, strategic SCN management. 

Question:
What data types are available at SCNBase?
Answer:
  • Genome assemblies
  • Gene models
  • Gene annotations
  • Repeat annotations
  • Transcriptome data
  • Effector data
  • Genetic maps (coming soon)
  • QTL data (coming soon)
Question:
How do I submit data to SCNBase?
Answer:

Please contact one of the website data curators via email.  There is likely a data curator from a group with whom you already collaborate.

Question:
Where can I download data?
Answer:

Data can be downloaded using the Downloads link on the homepage.  All data and corresponding metadata currently available in SCNBase is available here.

Use the search bar to narrow down the data your search for the data you wish to...

Question:
What is SCNBase?
Answer:

SCNBase is a website designed as a centralized knowledge base for SCN researchers and producers.  It contains genomics, genetics, population data along tools to translate this information in to practical applications.  SCNBase uses...