IGB Release Documentation
Page tree

Versions Compared

Old Version 505

changes.mady.by.user Paige Kulzer

Saved on

compared with

New Version Current

changes.mady.by.user Nowlan Freese

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  • The added Quickload site is available for the H_Sapien_Dec_2013 genome in the Available Data section.
  •  mac
  •  linux
  •  windows


Verify that all files in the Quickload site are loading into IGB (Data set names may differ from below - that's OK)

...

    •  pacBio.bam
      chr1:9,971-10,034
      click Load Sequence to load sequence data and create track (gray), click Load Data to load data into it
      * note: sequence reads are imported in variable order, so your view may differ from the image below. Simply ensure that the gray portion of the reads
        is consistently on the left side and generally aligns to the gray portion of the reference sequence (the NNNN portion) at the bottom, as well as that no 
        artifacts are present in your view that are not in the image below. Check here for more details.  
    •  
  • Bed
    •  Bed_HomoSapien.bed
    •  Bed_HomoSapien.bed.gz
      chr1:1,699,059-1,912,174
  • BedGraph
    •  BedGraph_HomoSapien.bedgraph
    •  BedGraph_HomoSapien.bedgraph.gz
      chr1:386,893-7,895,983
  • BigBed
    •  BigBed_HomoSapien.bigbed
      chr1:1,735,393-2,060,653
  • BigWig
    •  BigWig_HomoSapien,bigwig
      chr1:1,735,393-2,060,653
  • CRAM
    •  NB72462M_HomoSapien.cram

...

  • GFF3
    •  GFF3_HomoSapien.gff3
    •  GFF3_HomoSapien.gff3.gz
      chr1:1,735,393-2,060,653
  • GTF
    •  GTF_HomoSapien.gtf
    •  GTF_HomoSapien.gtf.gz
  • NarrowAndBroadPeak
    •  BroadPeak_HomoSapien.broadpeak
    •  BroadPeak_HomoSapien.broadpeak.gz
      chr1:800,118-800,619


    •  NarrowPeak_HomoSapien.narrowpeak
    •  NarrowPeak_HomoSapien.narrowpeak.gz
      chr1:9,361,070-9,361,207


      chr1:0-12,643,524
  • Sam
    •  Sam_HomoSapien_withHeader.sam 
      chr1:85,234,475-85,234,620
      Load data and sequence
  • VCF
    •  VCF_HomoSapien.vcf
    •  VCF_HomoSapien.vcf.gz
      chr1:1,234,555-1,234,601
  • Wig
    •  Wig_HomoSapien.wig
    •  Wig_HomoSapien.wig.gz
      chr1:37,750,880-38,042,899

...

  • Single base mismatches of A, T, C, and G appear with a color scheme that matches the sequence in the coordinate axis (the bottom).
  •  mac
  •  linux
  •  windows
  • Deletions appear as shown, a line with an arrow (they used to appear as a gray space with a dash in v9.0.2 and earlier).
  •  mac
  •  linux
  •  windows
  • Insertions appear as shown (see position 7,319,310 in image)
  •  mac
  •  linux
  •  windows