support for more genomes [igvR]
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Peng ▴ 20
@peng-24004
Last seen 10 months ago

I'm a new user of igvR and finds it a perfect tools to visualize my interested regions in R! Just a follow-up on the plan to support custom genomes, it would be great if the following method can be added


setCustomGenome(igv, name="TAIR10",
                fastaURL="https://myHost.net/tair10/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa",
                indexURL="https://myHost.net/tair10/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.fai",
                aliasURL: "https://myHost.net/tair10/chromosomeAliases.txt",
                annotationURL: "https://myHost.net/TAIR10_genes.sorted.chrLowered.gff3.gz")

I'd be definitely interested in giving it a try if possible!

Thanks!

igvR • 351 views
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Working on this now. thanks for the nudge, Peng.

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Paul Shannon ▴ 460
@paul-shannon-5944
Last seen 9 weeks ago
United States

igvR in devel, version 1.11.1, has the new method, setCustomGenome. A vignette is coming soon. Man page for the function is in the package, and two examples are in inst/unitTests/test_setCustomGenome, of which this is the all-parameters-specified version, using hg38 files offered on amazon by the Broad:

 setCustomGenome(igv,
                 id="hg38",
                 genomeName="Human (GRCh38/hg38)",
                 fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
                 fastaIndexURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
                 cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
                 chromosomeAliasURL=NA,
                 geneAnnotationName="Refseq Genes",
                 geneAnnotationURL="https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz",
                 geneAnnotationTrackHeight=500,
                 geneAnnotationTrackColor="red",
                 initialLocus="chr5:88,621,308-89,001,037",
                 visibilityWindow=5000000)
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igvR version 1.11.2 in devel has this feature, as demonstrated in a new vignette: 1

The vignette also explains how to start a simple local webserver, with byte ranges and CORS headers.

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That is great! Thanks a bunch Paul!

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