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: https://quickload-testing.s3.amazonaws.com/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
         •  
           
           
           
       • 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
         •  
       • 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
           
       • GFF3
         •  GFF3_HomoSapien.gff3
         •  GFF3_HomoSapien.gff3.gz
           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 
           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

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)