Versions Compared

Old Version 2

changes.mady.by.user upendra kumar Devisetty

Saved on

compared with

New Version Current

changes.mady.by.user upendra kumar Devisetty

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Panel
borderColor#ccc
bgColor#FFFFCE
titleBGColor#F7D6C1
titleAlert:
borderStyledashed

Image Removed

 

The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need anapp reinstated, please contact support@cyverse.org.

The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on to the bottom of this page. Or send comments per email to upendra@cyversesupport@cyverse.org. Thank you.

Rationale and background: 

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files using template for submission to GenBank. Additional manual editing is not required before submission.

...

  1. Template file containing a text ASN.1 Submit-block object (suffix .sbt).
  2. Nucleotide sequence data in FASTA format (suffix .fsa). Can be either a single fasta file (containing a single sequence) or single fasta file (containing multiple sequences) 
  3. Output file namefilename

Optional

  1. Feature Table or Annotation file (suffix .tbl). [Required only if including annotation]
  2. Structured comment file (suffix .cmt)

...

The test data are provided for testing tbl2asn (ungapped)-25.3 8 in here - /iplant/home/shared/iplantcollaborative/example_data/tbl2asn.sample.data:

Use the following inputs/outputs and parameters for testing tbl2asn (ungapped)-25.38

  1. Mandatory argument

    1. Template file - template_BP_BS.sbt

    2. Fasta file - multiple.fsa
    3. Output file - multiple.sqn
  2. Optional arguments 
    1. Annotation file - multiple.tbl
    2. Structured comment file - assembly.cmt
  3. Parameters
    1. Organism name - [organism=Helicobacter pylori ABC1] [strain=ABC1] [host=Homo sapiens] [isolation-source=blood]
    2. Master Genome Flag - n (default)
    3. Run Discrepency report - checked (default and recommended) 

Output Reports:

  1. multiple.sqn - sqn file for submission to WGS
  2. multiple.val - varification report
  3. discrep - discrepency report
  4. errorsummary.val - Summary file showing the number, severity and type of errors found in all the .val files.

 

More information about tbl2asn (ungapped)-25.3 8 can be found at http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

...