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To do the conversion that we want, use this command:

Code Block
cds
mkdir IGV_Tutorial
java -cp /corral-repl/utexas/BioITeam/bin/readseq.jar run $SCRATCH/bowtie2MappingTutorial/NC_012967.1.gbk -f GFF -o NC_012967.1.gbk.gff

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The easiest way to to this is probably to copy everything you want to transfer into a new directory called IGV_export. Since many of the tutorial output files had the same names (but resided in different directories) be careful to give them unique destination names when you copy them into the new directory together. To ensure you don't overwrite things be sure to use the -n command on the cp option.

While your instinct may be to use the cd command for much of this, try to stick to using the cp -n command with For starters, you could change into your mapping directory and run commands like these if you just came from the mapping tutorial:

Code Block
mkdir IGV_export
cp NC_012967.1.fastagbk.gff IGV
cp NC_012967.1.fasta.fai IGV
cp _export  # copy the new file you just converted to the export directory
cp $SCRATCH/bowtie2MappingTutorial/bowtie2/NC_012967.1.gbk.gff IGV
cp bowtiefasta IGV_export
cp $SCRATCH/bowtie2MappingTutorial/bowtie2/NC_012967.1.fasta.fai IGV_export
cp $SCRATCH/bowtie2MappingTutorial/bowtie2/SRR030257.sorted.bam IGV_export/bowtie.sorted.bam
cp bowtie$SCRATCH/bowtie2MappingTutorial/bowtie2/SRR030257.sorted.bam.bai IGVIGV_export/bowtie.sorted.bam.bai
tar -czvf IGV_export.tar..gz IGV_export

Now, copy this the entire compressed IGV directory back to your local Desktop machine.

Remember how? Try it on your own first, before peeking...
Expand
Remember how? Try it on your own first, before peeking...
titleAnother refresher on how to copy files back from lonestar

In the terminal connected to Lonestar, figure out the complete path to the IGV directory.

Code Block
pwd

Open a new terminal window on your Desktop. Fill in the parts in brackets <> in this command:

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scp -r <username>@lonestar.tacc.utexas.edu:</full/path/to/IGV/><full_path_to_IGV>/IGV_export.tar.gz .

Anchor
Launching IGV
Launching IGV

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We're really interested in places in the genome where we think there are mutations. If you have completed the In the Variant calling tutorial we identified such locations but lacked a good way to visualize them. This is your opportunity to visualize them. First transfer the bowtie2.vcf file back to your local computer, then you can load your VCF files to check out those spots, but first before you can do that you you need to (guess what?) index it.

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