General Function Checklist

Verify that all commonly used file formats are properly supported in IGB by loading all files available on the Smoke Testing Quickload.

1. Navigate to the Data Sources tab in Preferences.
2. Add a Data Source using the following URL: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/

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

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

• Bam
  • Bam_HomoSapien.bam 
    go to region: chr1:1,695,935-1,696,076
    click Load Sequence to load sequence data and create track (gray), click Load Data to load data into it
    
    
    
• Bam - PacBio with softclipping

• • 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

chr2:124,477,335-124,477,438

• 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
    

Sequence appearance

1. Open the A_thaliana_Jun_2009 genome.
2. From the RNA-Seq quicklaod (available by default as of 9.0.1), open the file RNA-Seq / Pollen SRP022162 / Reads / Pollen alignments.  (url http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP022162/Pollen.bam)
3. Go to location: Chr1:7,313,640-7,319,896
4. Load Data and Load Sequence.  Make sure the +/- option is checked for both the TAIR10_mRNA track (loaded by default) and the Pollen alignments track.
5. Go to location: Chr1:7,319,301-7,319,375
6. Optimize the stack height, and compare the main view to this image:

• Single base mismatches of A, T, C, and G appear with a color scheme that matches the sequence in the coordinate axis (the bottom).

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• 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).

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• Insertions appear as shown (see position 7,319,310 in image)

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