IGV with all data produced by Scrimer

_images/igv.png

Tracks, from top to bottom:

  • genome navigator, ‘genome’ produced in Map contigs to the reference genome
  • alldup.bam coverage - total coverage for the region, produced in Map reads to the scaffold
  • lx5-variants-selected.vcf.gz - summary of the variants, filtered variants are shown in lighter color, produced in Detect and choose variants
  • sample list - provides detailed information on variants in each sample
  • alldup.bam - details on coverage and SNP (colored) / INDEL (black), in the context menu choose Group alignments by > sample and Color alignments by > read group, produced in Map reads to the scaffold
  • sequence
  • lx5-primers.gff3 - resulting primers, hover with mouse for details on calculated properties, produced in Design primers
  • lx5.sorted.gff3.gz - annotations for the scaffold - predicted and transferred exons, produced in Map contigs to the reference genome
  • floating window with a list of designed primers, produced in Design primers

How to get to this view

  • run IGV (version 2.2 is used here)
  • Genomes > Load genome from file, choose your scaffold
  • load all the tracks by File > Load from File
  • rearrange tracks according to your preference by dragging the label with the mouse
  • choose Regions > Import Regions, pick the .bed file created in Design primers, choose Regions > Region Navigator