jbrowse基因组浏览器部署

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参考文档
jbrowse2部署方式：https://jbrowse.org/jb2/docs/quickstart_web/

准备一台Linux服务器，建议配置2c4G，磁盘100G，lvm类型，后续不够可以扩容

一、jbrowse部署

1.1 jbrowse部署

sudo mkdir /var/www/jbrowse;
sudo chown `whoami` /var/www/jbrowse;

下载安装包

fetch a JBrowse release zip file
curl -O http://jbrowse.org/releases/JBrowse-1.8.0.zip

# unzip it and cd into it
unzip JBrowse-1.8.0.zip
cd JBrowse-1.8.0
mv JBrowse-1.8.0/jbrowse  /var/www/html  #将项目移动到静态文件目录，后边用ng加载

1.2 nginx配置

nginx安装

yum -y install nginx   #centos安装
// 更新包
sudo apt-get update   #ubuntu安装nginx
// 下载安装nginx
sudo apt-get install nginx #ubuntu安装nignx

nginx配置

  server {
        listen       80 default_server;
        listen       [::]:80 default_server;
        server_name  _;
        #root         /var/www/html/jbrowse;

        # Load configuration files for the default server block.
        include /etc/nginx/default.d/*.conf;

        location / {
        root  /var/www/html/jbrowse;
        autoindex on;
        index  index.html index.htm  index.jsp;
        }

        error_page 404 /404.html;
            location = /40x.html {
        }

启动nginx

systemctl enable nginx
systemctl start nginx

二、数据导入

1、 ca文件处理

samtools工具安装

 wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
  tar -jxvf samtools-1.9.tar.bz2 
  cd samtools-1.9/
  ./configure --prefix=/usr/local/samtools #编译
  make 
  make install

samtools faidx zdd0006.genome.v1.fa #生成ca文件的索引
执行命令后会自动生成文件zdd0006.genome.v1.fa.fai

2、vcf格式文件处理

确保你的 VCF 文件是经过 BGZF 压缩的（以 .vcf.gz 结尾），并且已经创建了相应的索引文件（.tbi 文件）。如果没有，你可以使用 bgzip 和 tabix 工具来进行压缩和索引。
tabix命令安装

git clone https://github.com/samtools/htslib.git
 git submodule update --init --recursive

然后进入项目make 和make install
数据处理

 bgzip -c 680_sample_filter_ID.vcf > 680_sample_filter_ID.vcf.gz
 tabix -p vcf 680_sample_filter_ID.vcf.gz

3.gff文件

gff文件索引
使用GFF3文件构建索引，在建立索引之前需要对GFF3文件进行排序，安装染色体和位置进行排序

##排序

 grep -v "^#"  Gmax_275_Wm82.a2.v1.gene1.gff3  |sort -k1,1 -k4,4n >Gmax_275_Wm82.a2.v1.gene1.gff3

在排序完成后进行压缩和建立索引；使用tabix软件进行；

tabix安装参考 https://www.jianshu.com/p/b6f885fc8b5f
##压缩文件
bgzip Gmax_275_Wm82.a2.v1.gene1.gff3
##建立索引
tabix -p gff Gmax_275_Wm82.a2.v1.gene1.gff3.gz
在tracks.conf文件中添加配置信息

[tracks.genes]
urlTemplate=Ghirsutum_HZAU_V1.0_gene.gff3.gz
storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
type=CanvasFeatures

4.Bam格式文件

##对bam文件排序

samtools sort test.bam -O bam -o test_sort.bam

##构建索引

samtools index test_sort.bam

在tracks.conf文件中添加配置信息

[tracks.alignments]
urlTemplate=test_sort.bam
storeClass=JBrowse/Store/SeqFeature/BAM
type=Alignments2

4.最终配置如下

track.conf配置如下

[GENERAL]
refSeqs=Gmax_275_v2.0.fa.fai
[tracks.Gmax_275_v2_0]
urlTemplate=Gmax_275_v2.0.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence


refSeqs=SN14.genome.fa.fai
[tracks.SN14_genome]
urlTemplate=SN14.genome.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence

refSeqs=genome.v1.fa.fai
[tracks.zdd0006_genome_v1]
urlTemplate=zdd0006.genome.v1.fa
storeClass=JBrowse/Store/SeqFeature/IndexedFasta
type=Sequence


[tracks.680_sample_filter_ID]
# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate    = 680_sample_filter_ID.vcf.gz

 
# settings for how the track looks
category = VCF
type = JBrowse/View/Track/CanvasVariants
key  = 680_sample

[tracks.Gmax_309samples_wm82_mind02geno02maf005]
# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate    = Gmax_309samples_wm82_mind02geno02maf005.snp.vcf.gz


# settings for how the track looks
category = VCF
type = JBrowse/View/Track/CanvasVariants
key  = Gmax_309samples_wm82_mind02geno02maf005


[tracks.wm82]
urlTemplate=Gmax_275_Wm82.a2.v1.gene1.gff3.gz
storeClass=JBrowse/Store/SeqFeature/GFF3Tabix
type=CanvasFeatures

数据查看

二、FAQ

采用jbrowse2方式部署，track文件应该在当前工程目录，目录格式如下

(base) [root@iZuf6dz2cdbu61cqxlgdknZ jbrowse2]# samtools faidx PdeltoidesWV94_445_v2.
PdeltoidesWV94_445_v2.0.fa                PdeltoidesWV94_445_v2.1.gene.gff3.gz      PdeltoidesWV94_445_v2.1.gene.gff3.gz.tbi  
(base) [root@iZuf6dz2cdbu61cqxlgdknZ jbrowse2]# samtools faidx PdeltoidesWV94_445_v2.0.fa 
(base) [root@iZuf6dz2cdbu61cqxlgdknZ jbrowse2]# jbrowse add-assembly  PdeltoidesWV94_445_v2.0.fa --load copy --out .
Added assembly "PdeltoidesWV94_445_v2.0" to config.json
(base) [root@iZuf6dz2cdbu61cqxlgdknZ jbrowse2]# ls

目录结构

参考资料
1、https://jbrowse.org/docs/tutorial.html
2、https://jbrowse.org/jb2/docs/quickstart_web/