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You can start this tutorial two ways:
- *If you have an
intro_to_mappingdirectory with output from the previous tutorials with aligned reads or variant calls Mapping tutorial or the Variant calling tutorial, then you should use those files for this tutorial. - If you do not have any results, you can use some "canned" ones that we provide. Copy the entire contents of this directory back to your local machine:
Then skip down to #Launching IGV.Code Block $BI/ngs_course/intro_to_mapping/IGV
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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 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.
The resulting jag1_blast.out.gff can be moved to your local machine and opened in IGV. Load the human reference first though! |
If you have only done the mapping tutorial and NOT the variant calling tutorial
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 in the Variant calling tutorial. If you are in your
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samtools faidx NC_012967.1.fasta
samtools view -b -S -o bowtie/SRR030257.bam bowtie/SRR030257.sam
samtools sort bowtie/SRR030257.bam bowtie/SRR030257.sorted
samtools index bowtie/SRR030257.sorted.bam
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Repeat the last three commands for each SAM output file that you want to visualize in IGV.
Copy files to your desktop
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- Indexed reference FASTA files
- GFF reference sequence feature files
- Sorted and indexed mapped read BAM files
- VCF result files
- ... and possibly many other types of files.
We're going to copy all of these The easiest way to to this is probably to copy everything you want to transfer into a new directory called IGV to make it easier to just transfer the ones that we want. Change . 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.
For starters, you could change into your intro_to_mapping directory and run commands like these commands if you just came from mappingthe Mapping tutorial:
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mkdir IGV
cp NC_012967.1.gbk.gff IGV
cp bowtie/bowtie.sam IGV/bowtie.sam
cp bowtie2/bowtie2.sam IGV/bowtie2.sam
cp bwa/SRR030257.sam IGV/bwa.sam
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| If you just came from variant calling, you can run these instead... | If you just came from variant calling, you can run these instead... | Add these: Code Block | fasta IGV cp NC_012967.1.gbk fasta.gff fai IGV cpsamtools_bowtie/ NC_012967.1.fasta IGV
cp samtools_bowtie/NC_012967.1.fasta.fai IGV
cp samtools_bowtie2/SRR030257.sorted.bam IGV/bowtie2.sorted.bam
cp samtools_bowtie2/SRR030257.sorted.bam.bai IGV/bowtie2.sorted.bam.bai
cp samtools_gbk.gff IGV cp bowtie/SRR030257.sorted.bam IGV/bowtie.sorted.bam cpsamtools_ 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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Now, copy this entire IGV directory back to your local Desktop machine.
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We're really interested in places in the genome where we think there are mutations. You If you have completed the Variant calling tutorial, then you can load the your VCF file files to check out those spots, but first you need to (guess what?) index it.
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