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(NB: I had to "fix" bp_genbank2gff3.pl to work on our GenBank file, by removing a line in the Perl script that caused an error. If someone knows of an easier way to get a GFF file from a file downloaded from Genbank, please share!)

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Side-note on displaying BLAST results as GFF files in IGV or other browsers
Side-note on displaying BLAST results as GFF files in IGV or other browsers

Another useful trick with either IGV or UCSC: displaying your own BLAST results: BioPerl allows for super-easy conversion from blast output to a gff file; IGV and the UCSC browser both understand GFF files. The short script bl2gff.pl does the conversion.

Let's use the blast result we had from the earlier test for the JAG1 gene to show you how. You'll need to provide the input file - it's the ".oNNNNNN" output file from your blast job.

Code Block
titleDisplaying BLAST results in IGV or UCSC

grep '^gi' blast_jag1.o586038 > jag1_blast.out
module load perl
module load bioperl
/corral-repl/utexas/BioITeam/bin/bl2gff.pl jag1_blast.out > jag1_blast.out.gff

The resulting jag1_blast.out.gff can be moved to your local machine and opened in IGV. Load the human reference first though!

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  • Check out the rbsA gene region? What's going on here?
  • What is going on in the pykF gene region? You might see red read pairs. What does that mean?
  • Go to coordinate 2,698,092. Compare the bowtie and BWA alignments. Can you explain what's going on here?
  • Go to coordinate 475,263. ompare the bowtie and BWA alignments. What's the story here?

Advanced exercise: human data scavenger hunt

Data from the CEU trio from the 1000 Genomes Project can be found directly from the Broad's server for IGV.

Find the dbSNP accession number for the SNP apparent in the two 1000 genomes project trios in the intron between exons 8 and 9 of the GABBR1 gene.

Steps:

  1. Download and install the Integrative Genome Viewer from the Broad Institute.
  2. Select "Human hg18" as the reference genome
  3. Get some data: File -> “Load from Server…” -> 1000 genomes -> CEU and YRI trios
  4. Find the gene and the right exons
  5. Zoom in until you find the SNP
  6. Load and look at the SNP track: File -> Load from server -> Annotations -> Variants -> dbSNP

This is whole genome coverage data; later we'll look at exome data.

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Answer
Answer

rs29220