jbrowse2 [idx_check_range] Region cannot be stored in a tbi index. Try using a csi inde

原创已于 2024-02-26 21:09:48 修改 · 561 阅读

9 ·

CC 4.0 BY-SA版权

文章标签：

#开发语言

于 2024-02-26 20:57:36 首次发布

本文介绍了如何在JBrowse中操作，包括使用Cbgzip压缩的bed.gz文件、csi索引、创建软链接以及修改config.json来加载和管理遗传学数据，特别是针对Aegilops_tauschii基因组的数据。

加上-C
bgzip file.bed
tabix -C file.bed.gz
jbrowse add-track file.bed.gz --out /usr/local/jbrowse/mydata/ --load copy
也可以不用–load copy 使用 --load symlink 建立软连接

建立软连接
ln -s 原地址新地址

ln -s /media/data/jb2fa/Aegilops_tauschii.bed.gz.csi  /var/www/html/jbrowse2/Aegilops_tauschii.bed.gz.csi

修改config.json

{
  "assemblies": [
    {
      "name": "Aegilops_tauschii",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Aegilops_tauschii-ReferenceSequenceTrack",
        "adapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "Aegilops_tauschii.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "Aegilops_tauschii.fa.fai",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {},
  "connections": [],
  "defaultSession": {
    "name": "New Session"
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "63_Aegilops_tauschii.bed",
      "name": "63_Aegilops_tauschii.bed",
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "63_Aegilops_tauschii.bed.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "63_Aegilops_tauschii.bed.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": [
        "Aegilops_tauschii"
      ]
    }
  ]
}