How to use (if using the previous version, check here)



Views

Tracks
Tasuke_screenshot

Frequency Mode
Tasuke_screenshot

Absolute position mode

Tasuke_screenshot


snpEff Mode

Tasuke_screenshot


Effect category

Tasuke_screenshot


View of 1bp Scale

Tasuke_screenshot


Annotation track

Tasuke_screenshot



Action

Search & Jump
Tasuke_screenshot


Move
Tasuke_screenshot

Zoom
Tasuke_screenshot

System phylogenetic tree
Tasuke_screenshot

Tools

Design PRIMER
  1.Open setting dialog
PRIMER_screenshot


  2.Parameter setting
    2-1.Main settings PRIMER_screenshot


    2-2.General settings(Optional) PRIMER_screenshot


    2-3.ePCR settings(Optional) PRIMER_screenshot


  3.Result
    3-1.Result PRIMER_screenshot


    3-2.Jump BLAST with primer PRIMER_screenshot


    3-3.Move to the perimer designing position PRIMER_screenshot


    3-4.ePCR Result PRIMER_screenshot


    3-5.Download Result PRIMER_screenshot


    3-6.Download Result(using ePCR) PRIMER_screenshot

Create Phylogenetic Tree
If the accession name is set to "Name" display, the phylogenetic tree may not be displayed correctly. If so, change it to "ID" in the AccessionManager.

  1.Open setting dialog
PRIMER_screenshot


  2.Parameter setting
    2-1.Main settings(with Chromosome and Position) PRIMER_screenshot


    2-2.Main settings(with GeneID) PRIMER_screenshot


  3.Result
    3-1.Result PRIMER_screenshot


    3-2.Change Circle phylogram PRIMER_screenshot


    3-3.Change Cladogram PRIMER_screenshot


    3-4.Sort snpblock table PRIMER_screenshot


    3-5.Download tree data PRIMER_screenshot


    3-6.Select Accession (option) PRIMER_screenshot

BLAST
  1.Open setting dialog
PRIMER_screenshot


  2.Parameter setting
    2-1.Main settings PRIMER_screenshot


    2-2.Alignment Options PRIMER_screenshot


  3.Result
    3-1.Result PRIMER_screenshot


    3-2.BLAST result using primer PRIMER_screenshot


    3-3.Jump alignment section of BLAST result PRIMER_screenshot



GWAS
  1.Open GWAS dialog
GWAS_screenshot


  2.Show information
GWAS_screenshot


  3.Zoom in manhattan plot
GWAS_screenshot


  4.Zoom out manhattan plot
GWAS_screenshot


  5.Pan manhattan plot
GWAS_screenshot


  6.Change chromosome
GWAS_screenshot


  7.Change phenotype
GWAS_screenshot


  8.Filter By SnpEff impact
GWAS_screenshot


  9.Sort By Position
GWAS_screenshot


  10.Move postiion on GWAS plot
GWAS_screenshot


  11.Move postiion on variant list
GWAS_screenshot