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