Example input and output files for the virus variant caller pipeline

example_config_files.zip: reference annotations for HSV-1 strain 17 and config files describing the input files.

example_bam_files.zip: alignment files (in BAM format) for two replicates each of the  ICP0 and vhs knockout mutants.

example_fastq_files.zip: read sequences (in FASTQ format) for two replicates each of the  ICP0 and vhs knockout mutants.

example_output.zip: resulting output files

After downloading and unpacking the zip-archives, adjust the constants in the Watchdog workflow as follows:

<const name="REFERENCE">/path/to/chrHsv1_s17.fa</const><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const><const name="CONFIG">/path/to/config_strains_HSV1.txt</const><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const><const name="samples">/path/to/example_samples.txt</const><const name="replicates">/path/to/example_replicates.txt</const>

where /path/to/ is the directory the content of the archive zip-archives is located in.

Furthermore, change /path/to/ in the example_replicates.txt  and example_samples.txt files to the directory the content of the archive zip-archives is located in.

`example_config_files.zip`: 用于单纯疱疹病毒1型（Herpes Simplex Virus 1，简称HSV-1）17毒株的参考注释文件，以及描述输入文件的配置文件。
`example_bam_files.zip`: 包含ICP0与vhs基因敲除突变体各两个生物学重复的比对文件（二进制比对映射格式，简称BAM）。
`example_fastq_files.zip`: 包含ICP0与vhs基因敲除突变体各两个生物学重复的测序读段序列（FASTQ格式）。
`example_output.zip`: 最终生成的输出文件。

下载并解压所有压缩归档文件后，请按如下方式修改Watchdog工作流（Watchdog Workflow）中的常量配置：
<const name="REFERENCE">/path/to/chrHsv1_s17.fa</const><const name="REFERENCE_SNPS">/path/to/reference_snps.txt</const><const name="CONFIG">/path/to/config_strains_HSV1.txt</const><const name="GTF">/path/to/HSV1_Annotation_chrHsv1_s17.gtf</const><const name="samples">/path/to/example_samples.txt</const><const name="replicates">/path/to/example_replicates.txt</const>

其中`/path/to/`指代所有压缩归档文件解压缩后的存储目录。

此外，请将`example_replicates.txt`与`example_samples.txt`文件中的`/path/to/`替换为上述压缩归档文件的解压目录路径。