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:
       
       • Bam
         • Bam_HomoSapien.bam
           
       • Bed
         • Bed_HomoSapien.bed
         • Bed_HomoSapien.bed.gz
           
           
           
       • BedGraph
         • BedGraph_HomoSapien.bedgraph
         • BedGraph_HomoSapien.bedgraph.gz
           
       • BigBed
         • BigBed_HomoSapien.bigbed
           
       • BigWig
         • BigWig_HomoSapien,bigwig
           
       • GFF3
         • GFF3_HomoSapien.gff3
         • GFF3_HomoSapien.gff3.gz
       • GTF
         • GTF_HomoSapien.gtf
         • GTF_HomoSapien.gtf.gz
       • NarrowAndBroadPeak
         • BroadPeak_HomoSapien.broadpeak
         • BroadPeak_HomoSapien.broadpeak.gz
           
         • NarrowPeak_HomoSapien.narrowpeak
         • NarrowPeak_HomoSapien.narrowpeak.gz
           
       • VCF
         • VCF_HomoSapien_Mutations(SNPs).vcf
         • VCF_HomoSapien_Mutations(SNPs).vcf.gz
           • Can you see mutations (SNPs)?
             
         • VCF_HomoSapien_InsertionsAndDeletions.vcf
         • VCF_HomoSapien_InsertionsAndDeletions.vcf.gz
           • Can you see deletions?
             
           • Can you see insertions?
             
       • Wig
         • Wig_HomoSapien.wig
         • Wig_HomoSapien.wig.gz

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:   Chr1:7,319,301-7,319,375

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)