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- Indexed reference FASTA files
- GFF reference sequence feature files
- Sorted and indexed mapped read BAM files
- VCF result files
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| title | You will want the contents of these directories plus the *.gff file that we just made |
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We're going to copy all of these into a new directory called IGV to make it easier to just transfer the ones that we want.
| Code Block |
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mkdir IGV
cp NC_012967.1.gbk.gff IGV
cp samtools_bowtie/NC_012967.1.fasta IGV
cp samtools_bowtie/NC_012967.1.fasta.fai IGV
cp samtools_bowtie/SRR030257.sorted.bam IGV/bowtie.sorted.bam
cp samtools_bowtie/SRR030257.sorted.bam.bai IGV/bowtie.sorted.bam.bai
cp samtools_bwa/SRR030257.sorted.bam IGV/bwa.sorted.bam
cp samtools_bwa/SRR030257.sorted.bam.bai IGV/bwa.sorted.bam.bai
cp comparison/* IGV
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Launching IGV
Navigate a web browser to this page: http://www.broadinstitute.org/software/igv/download
Go ahead and click on the "Launch with 2 GB" option. This will download a "Java Web Start" file that you can launch by locating on your Desktop and double-clicking.
Import to IGV.
From the main window of IGV, click on File -> Import Genome and you should be presented with the following window.
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