Tumbling Oysters - Working with IGV

Need to index genome

/home/shared/samtools-1.12/samtools faidx ../data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fna

/home/shared/samtools-1.12/samtools faidx ../data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fa

start of IGV (save as xml)

<Session genome="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fa" hasGeneTrack="false" hasSequenceTrack="true" locus="NC_082382.1:6171230-6590510" version="8">
    <Resources>
        <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gff" type="gff"/>
        <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gtf" type="gtf"/>
    </Resources>
    <Panel height="807" name="FeaturePanel" width="1500">
        <Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="POSITIVE" shouldShowTranslation="false" visible="true"/>
        <Track attributeKey="genomic.gtf" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gtf" name="genomic.gtf" visible="true"/>
        <Track attributeKey="genomic.gff" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gff" name="genomic.gff" visible="true"/>
    </Panel>
    <PanelLayout dividerFractions="0.007334963325183374"/>
    <HiddenAttributes>
        <Attribute name="DATA FILE"/>
        <Attribute name="DATA TYPE"/>
        <Attribute name="NAME"/>
    </HiddenAttributes>
</Session>

--- title: "Working with IGV" description: "for cod" categories: [R, igv, cod] # self-defined categories #citation: date: 05-23-2024 author: - name: Steven Roberts url: orcid: 0000-0001-8302-1138 affiliation: Professor, UW - School of Aquatic and Fishery Sciences affiliation-url: https://robertslab.info #url: # self-defined image: https://gannet.fish.washington.edu/seashell/snaps/IGV_2024-05-24_10-33-08.png # finding a good image draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready! format: html: code-fold: true code-tools: true code-copy: true highlight-style: github code-overflow: wrap --- Need to index genome ``` bash /home/shared/samtools-1.12/samtools faidx ../data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fna ``` ``` bash /home/shared/samtools-1.12/samtools faidx ../data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fa ``` start of IGV (save as xml) <Session genome="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/GCF_031168955.1_ASM3116895v1_genomic.fa" hasGeneTrack="false" hasSequenceTrack="true" locus="NC_082382.1:6171230-6590510" version="8"> <Resources> <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gff" type="gff"/> <Resource path="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gtf" type="gtf"/> </Resources> <Panel height="807" name="FeaturePanel" width="1500"> <Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="POSITIVE" shouldShowTranslation="false" visible="true"/> <Track attributeKey="genomic.gtf" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gtf" name="genomic.gtf" visible="true"/> <Track attributeKey="genomic.gff" clazz="org.broad.igv.track.FeatureTrack" fontSize="10" groupByStrand="false" id="https://gannet.fish.washington.edu/seashell/bu-github/project-cod-temperature/data/ncbi_dataset/data/GCF_031168955.1/genomic.gff" name="genomic.gff" visible="true"/> </Panel> <PanelLayout dividerFractions="0.007334963325183374"/> <HiddenAttributes> <Attribute name="DATA FILE"/> <Attribute name="DATA TYPE"/> <Attribute name="NAME"/> </HiddenAttributes> </Session> ![](https://gannet.fish.washington.edu/seashell/snaps/IGV_2024-05-24_10-33-08.png)