General Function Checklist

Completed in:

• mac
• linux
• windows

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
           * 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
           
       • 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 line with an arrow (they used to appear as a gray space with a dash in v9.0.2 and earlier).
• Insertions appear as shown (see position 7,319,310 in image)