IGV.js | 载入自己下载的gtf文件

1.安装 htslib-1.20

https://www.htslib.org/doc/tabix.html

@J3$ cd ~/Downloads/
$ wget https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
$ tar jxvf htslib-1.20.tar.bz2

编译安装：
$ cd htslib-1.20/
$ ./configure --prefix=/home/wangjl/soft/htslib-1.20/
$ make -j16
$ make install

配置路径：
$ vim ~/.bashrc
export PATH=$PATH:/home/wangjl/soft/htslib-1.20/bin

测试：
$ source ~/.bashrc
$ which bgzip
~/soft/htslib-1.20/bin/bgzip
$ which tabix 
~/soft/htslib-1.20/bin/tabix

2. 生成fa和gtf的索引文件fa.fai, gtf.gz.tbi

$ cd /data/wangjl/scPolyA-seq2/ref/hg38/gencode/
$ (grep ^"#" GRCh38.p13.gtf; grep -v ^"#" GRCh38.p13.gtf | sort  -t $'\t' -k1,1V -k4,4n -k5,5n) | bgzip  > GRCh38.p13.sorted.gtf.gz

$ tabix -p gff GRCh38.p13.sorted.gtf.gz

$ samtools faidx input_ref.fa  #生成 input_ref.fa.fai

$ ls -lth
-rw-r--r--. 1 wangjl jinlab 370K Jul 24 20:03 GRCh38.p13.sorted.gtf.gz.tbi
-rw-r--r--. 1 wangjl jinlab  36M Jul 24 20:00 GRCh38.p13.sorted.gtf.gz
-rw-r--r--. 1 wangjl jinlab 905M May  1  2023 GRCh38.p13.gtf

-rw-r--r--. 1 wangjl jinlab  22K May  8  2023 GRCh38.p13.genome.fa.fai
-rw-r--r--. 1 wangjl jinlab 3.1G May  1  2023 GRCh38.p13.genome.fa

3.在IGV.js中引用资源

其他资源使用默认的，我已下载到服务器本地。

// refer in local: gencode
var hg38_local_gencode={
	"id": "hg38",
	"name": "Human (GRCh38/hg38)",
	"fastaURL": "ref/hg38/gencode/GRCh38.p13.genome.fa", //?someRandomSeed=0
	"indexURL": "ref/hg38/gencode/GRCh38.p13.genome.fa.fai",
	"cytobandURL": "ref/hg38/cytoBandIdeo.txt.gz",
	"aliasURL": "ref/hg38/hg38_alias.tab",
	
	"tracks": [
	  {
		"name": "GRCh38",
		"format": "gtf",
        "type": "annotation",
		"id": "hg38_genes",

		"url": "ref/hg38/gencode/GRCh38.p13.sorted.gtf.gz",
		"indexURL": "ref/hg38/gencode/GRCh38.p13.sorted.gtf.gz.tbi",

		"visibilityWindow": -1,
        //"visibilityWindow": 10000000, // 轨道的可见窗口大小
		"supportsWholeGenome": false,
		"removable": false,
		"order": 1000000,

		"height":250,   //height of ref track
		"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$"  //links to ncbi gene
	  }
	],
	"chromosomeOrder": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"
}


var options =
{
	//genome: "hg38",
	//init screen
	"locus": "chr21:45,512,381-45,521,866",
	
	reference:hg38_local_gencode,
	tracks: []
};

测试结果

• 上图：IGV默认的基因组注释文件ref/hg38/ncbiRefSeq.txt.gz
• 下图：我们导入的基因组注释文件 ref/hg38/gencode/GRCh38.p13.sorted.gtf.gz

两者在同一个地方还是有一些差异的：下图甚至多出一个转录本。

不过，不能评价哪个注释更可靠。毕竟都是知名学术机构发布的。

建议在一个项目中，使用最新的基因组注释文件，且

• 固定使用同一个机构、同一个版本号的gtf文件，
• 保证gtf和fa配对。