IGV create genome: cytoband not working
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2.2 years ago
nlehmann ▴ 130

I am building a genome file to visualize chicken data. I downloaded galGal6 genome and GTF from UCSC website and followed the instructions here: https://software.broadinstitute.org/software/igv/LoadGenome. I also want to add a cytoband, and downloaded a cytoband file from ucsc table browser as described here: https://software.broadinstitute.org/software/igv/Cytoband.

However, each time I try to add my cytoband file, an error appears saying that the genome could not be downloaded. The same data (genome + annotation) works fine when there is no cytoband.

Here is the top of the cytoband file:

#chrom  chromStart  chromEnd    name    gieStain
chr1    0   76608038    p   gneg
chr1    76608038    76858038    cen acen
chr1    76858038    77108038    cen acen
chr1    77108038    197608386   q   gneg
chr2    0   52151238    p   gneg
chr2    52151238    52401238    cen acen
chr2    52401238    52651238    cen acen
chr2    52651238    149682049   q   gneg
chr3    0   5801976 p   gneg

Here is the top of my GTF file:

chr1    galGal6_ensGene stop_codon  133973567   133973569   0.000000    -   .   gene_name "AFF3"; gene_id "ENSGALT00000075851.2"; transcript_id "ENSGALT00000075851.2";
chr1    galGal6_ensGene CDS 133973570   133973688   0.000000    -   2   gene_name "AFF3"; gene_id "ENSGALT00000075851.2"; transcript_id "ENSGALT00000075851.2";

Any help would be welcome

IGV RNA-Seq • 658 views
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Have you solved this problem?

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No I haven't, but was not too important

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