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You can start this tutorial two ways:
1. If you have an introduction intro_to_mapping directory with output from doing the previous tutorials with aligned reads or variant calls, then you can should use it those files for this tutorial.
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cd $SCRATCH/intro_to_mapping
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2. If you do not have the any results, you can copy some "canned" ones that we provide using these commands. Remove any existing intro_to_mapping directory in your $SCRATCH space before running these commands.
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. Copy the entire contents of this directory back to your local machine:
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$BI/intro_to_mapping/data intro_to_mapping cd intro_to_mapping cp -r $BI/ngs_course/intro_to_mapping/samtools_* . cp -r $BI/ngs_course/intro_to_mapping/comparison . igv |
Then skip down to #Launching IGV.
Prepare a GFF feature file for the reference sequence
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In the terminal connected to Lonestar, figure out the complete path to the IGV directory.
Open a new terminal window on your Desktop. Fill in the parts in brackets <> in this command:
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Launching IGV
There are two ways; Launching IGV in your web browser or by downloading the binaries locally and running IGV from your machine.
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Tip: You can also index BAM and FASTA files the same way inside of IGV if you haven't already created indexes for them. But, it's usually easier and quicker to do this on the command line.
Exercises
- 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. Compare the bowtie and BWA alignments. What's the story here?
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