IGV annotation issus

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Mar 22, 2025, 10:19:41 AM3/22/25

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I have tried to import my own-defined genome into IGV by creating JSON file. When load the genome file, it sucess to load the genome. And I can browser the genomic with correct annotation. However, it is not able to search the region by input a gene name. Do I do something wrong to my JSON file?

{
"id": "User_define",
"name": "User_define",
"fastaURL": "User_define.fa.gz",
"indexURL": "User_define.fa.gz.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz.tbi",
"indexed": false,
"order": 1000000,
"removable": false,
"visibilityWindow": -1
},
{
"name": "Own GTF file",
"format": "gtf",
"url": "User_define.gtf.gz",
"indexURL": "User_define.gtf.gz.tbi",
"order": 1000000,
"indexed": false,
"hidden": false
},
{
"name": "Viral Genome",
"format": "gtf",
"url": "User_define_virus.gtf.gz",
"indexURL": "User_define_virus.gtf.gz.tbi",
"order": 1000000,
"indexed": false,
"hidden": false
}
]
}

igv-help

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Mar 22, 2025, 10:35:58 AM3/22/25

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What version of IGV are you using?

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Mar 23, 2025, 2:14:28 AM3/23/25

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I am using the IGV 2.19.2 version. I tried two different versions but still the same. Below is a short list copy of my GTF file.

##description: evidence-based annotation of the human genome (GRCh38), version 32 (Ensembl 98)

##provider: GENCODE

##contact: gencod...@ebi.ac.uk

##format: gtf

##date: 2019-09-05

chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level >

chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocess>

chr1 HAVANA exon 12010 12057 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA transcript 12010 13670 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocess>

chr1 HAVANA exon 12179 12227 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 12613 12697 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 12975 13052 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 13221 13374 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 13453 13670 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseud>

chr1 HAVANA exon 14404 14501 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene>

chr1 HAVANA gene 14404 29570 . - . gene_id "ENSG00000227232.5"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; level 2; hgnc_id "H>

chr1 HAVANA transcript 14404 29570 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogen>

chr1 HAVANA exon 15005 15038 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene>

chr1 HAVANA exon 15796 15947 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene>

chr1 HAVANA exon 16607 16765 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene>

chr1 HAVANA exon 16858 17055 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene

igv-help 在 2025年3月22日星期六晚上10:35:58 [UTC+8] 的信中寫道：

James Robinson

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Mar 23, 2025, 3:51:59 PM3/23/25

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Yes there does seem to be an issue with searching from gtf and gff files. I will address it in the next release. As a workaround you could use our "hg38" reference and load your gtf files from the File menu. Or, simply changing your genome ID to "hg38" might work.

If you are able please open a git issue concerning this at https://github.com/igvteam/igv/issues.

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James Robinson

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Mar 23, 2025, 4:27:35 PM3/23/25

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Actually I spoke too soon, I had an unrelated configuration issue. Searching from a gtf file is working for me. Can you verify that the sequence names in your fasta file match the names in your gtf (e.g. chr1 in the snippet you provided)?

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