# 优化JBrowse

JBrowse的基本框架已经搭建好了，接下来就是使用它和sequenceServer以及配合数据库进行使用；前面那个教程是手动的配置索引文件，同样可以使用JBrowse自带的脚本进行配置；脚本运行的目录为`@/Jbrowse`，运行后将会在当前目录生成一个data文件夹

### 使用自带脚本进行格式化

脚本运行后将会

### 1.参考基因组文件

> 报错缺失对应的包，`Can't locate Digest/Crc32.pm in @INC`在网站下载后搬到那个目录就行

```bash
wget -c https://metacpan.org/raw/FAYS/Digest-Crc32-0.01/Crc32.pm?download=1
mkdir Digest
mv Crc32.pm  Digest/
##构建索引
./bin/prepare-refseqs.pl  --fasta ./Ghirsutum_HZAU_V1.1.fa --out Ghirsutum_genome_HAU_v1.1
```

修改对应的data目录下的trackList.json文件，进行配置

### 2.GFF3文件

同样的报错，下载对应的包，有个包很奇怪得用root使用`cpanm`重头编译

* `--trackLabel` json文件中对应字段的值，最终将会在`tracks`目录下生成对应的文件名

```bash
./bin//flatfile-to-json.pl  -gff ~/zpliu/sequenceServer/genomeData/Ghirsutum_genome_HAU_v1.1/Ghirsutum_gene_model.gff3  --trackType CanvasFeatures --compress --trackLabel Gene_annotion --out 指定输出目录
```

修改一下`json`文件中对应的分类和名称

* 设置成`HTMLFeatures`类型的话会更加方便点击

```javascript
      {
         "compress" : 1,
                 "category" : "Feature annotion",
         "key" : "Gene_annotion",
         "label" : "Gene_annotion",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature"
         },
         "trackType" : "CanvasFeatures",
         "type" : "CanvasFeatures",
         "urlTemplate" : "tracks/gff3/{refseq}/trackData.jsonz"
      }
```

### 3.BAM文件的JSON配置文件

```javascript
    {
      "category": "RNA-seq",
      "storeClass": "JBrowse/Store/SeqFeature/BAM",
      "urlTemplate": "./BAM/TM1_rmdup.bam",
      "type": "JBrowse/View/Track/Alignments2",
      "key": "leaf_SRR5886147"
    }
```

### 4.配置BigWig文件

> 文件说明 ：<https://www.cnblogs.com/djx571/p/12110883.html>
>
> <https://www.plob.org/article/9505.html>
>
> 配置参考: <http://jbrowse.org/docs/tutorial_classic.html#quantitative-tracks-bigwig-and-wiggle>

这个文件就是由BAM文件或者BED文件经过转换压缩后的二进制文件，能够直接在UCSC或者JBrowse文件中使用；在JBrowse中配置BigWig文件和配置BAM文件的流程差不多，这里不多做赘述。

## 建feature 索引 Index Names

在JBrowse加载后，为了能够实现对name或者geneID的搜索功能；就必须使用脚本将这些name和ID给建立索引；当有添加了新的feature时，就需要再运行一次`bin/generate-names.pl`

* `--out`输出目录
* `--tracks`对应的轨迹，多个轨迹之间用逗号隔开

```bash
##给gene注释建立索引，运行目录为@/data/Ghirsutum_genome_HAU_v1.1
../../bin/generate-names.pl  --out ./ -v  --tracks Gene_annotion
```


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://zpliu.gitbook.io/booknote/cottonweb/hou-duan/jbrowse-you-hua.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.