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. • Add a Data Provider to IGB using the following URL: http://igbquickload.org/smokeTestingQuickload/
     
     • The added Quickload site is available for the Homo sapien genome under the Available Data pane.
       
       
       
     • 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
         • 
           
         • Ensure soft-clipping can be hidden using the right-click menu, as shown below:
           
           
           
         •  
       • Bed
         • Bed_HomoSapien.bed
         • Bed_HomoSapien.bed.gz
           region: 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
           
       • GFF3
         • GFF3_HomoSapien.gff3
         • GFF3_HomoSapien.gff3.gz
           region: chr1:1,735,393-2,060,653
           

1. • • • 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 
           go to region: chr1:1,695,935-1,696,076
           To get the dark blue blocks you will need to load the sequence.
           The data in this file is identical to the Bam file above (Bam_HomoSapien.bam), it should appear identical to that.
       • VCF
         • VCF_HomoSapien.vcf
           chr1:1,234,555-1,234,601
           
       • Wig
         • Wig_HomoSapien.wig
         • Wig_HomoSapien.wig.gz
           chr1:37,750,880-38,042,899
           

Sequence appearance

Go to the Arabidopsis genome.  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)

Go to location: Chr1:7,313,640-7,319,896

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.

Go to location:   Chr1:7,319,301-7,319,375

Optimize the stack height, and compare the main view to this image:

Verify that:

• single base mismatches of A, T, C, and G appear with a color scheme that matches the sequence in the coordinate axis (the bottom).
• deletions appear as shown, a gray space with a dash.
• insertions appear as shown (see position 7,319,310 in image)