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  1. If you have a mapping directory with output from the Mapping tutorial and the SNV calling tutorial, then you should use those files for part 1 of this tutorial. You can proceed with either one alone or with both.
  2. Expand
    titleIf you have not done the other tutorials and want a "canned" data set provided for you, click here for example files.
    Code Block
    $BI/gva_course/mapping/IGV  # location of example files
cp -r /corral-repl/utexas/BioITeam/gva_course/mapping/IGV .  # example command to copy to current directory
scp -r username@ls5.tacc.utexas.edu:/corral-repl/utexas/BioITeam/gva_course/mapping/IGV . # to copy to a local computer skipping the step of copying to a lonestar directory and secure copying from there.

    Then skip down to #Launching IGV.

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  1. Download and install the Integrative Genome Viewer from the Broad Institute. 
  2. Select "Human hg19" as the reference genome from the top left drop down (you may need to select "more" to have hg19 as an option)
  3. Get some data: File > Load from Server… > 1000 genomes > Alignments > ACB > exome > HG01880
  4. Navigate to the rightmost exons of the GABBR1 gene.
  5. Zoom in until you find some SNPs. (Hint look just to the left of the 2nd exon).
  6. What type of library is this? (Hint: zoom out)
  7. If you knew this was a cancer patient, consider how strongly you would think this may be a potentially causative mutation.
  8. Imagine it was actually in the exon rather than just into the intron... would that make you consider it more?
  9. Load and look at the SNP track: File > Load from server > Annotations > Variants and Repeats > dbSNP 1.34.7
  10. The track may load with the Refseq genes, making it useful to resize that window to view both the gene and the dbSNP information simultaneously.
  11. Consider if this makes you think it more likely or less likely that this is a causative mutation.

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Expand
titleTo visualize mapped data without calling variants

You will need to index your reference FASTA and convert your SAM output files into sorted and indexed BAM files. The "why?" behind these steps is described more fully in the Variant calling tutorial. If you are in your mapping directory, these commands will perform the necessary steps.

Warning
titleSubmit to the TACC queue or run in an idev shell
Code Block
samtools faidx NC_012967.1.fasta
samtools view -b -S -o bowtie/SRR030257.bam bowtie/SRR030257.sam
samtools sort bowtie/SRR030257.bam -o bowtie/SRR030257.sorted
samtools index bowtie/SRR030257.sorted.bam

Repeat the last three commands for each SAM output file that you want to visualize in IGV.

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