SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta

Steps to generate the files in this data source:<br>1 - Clone the git repository at github.com/XuegongLab/neoguider and install according to the instructions on the github website. <br>2 - Download and extract the fastq files with accessions SRR7890830, SRR7890845, and SRR9134697; then, put the fastq files into the testdata directory.3 - run the following (this should take about three hours with 16 CPUs), you can go to the next step if you have manually put the corresponding file from this data source into testdata/results_from_fastq/SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta<br>snakemake --configfile config.yaml --config res=testdata/results_from_fastq/ prefix=SRR7890830-SRR7890845-SRR9134697 dna_tumor_fq1=testdata/SRR7890830_1.fastq.gz dna_tumor_fq1=testdata/SRR7890830_2.fastq.gz dna_normal_fq1=testdata/SRR7890845_1.fastq.gz dna_normal_fq2=testdata/SRR7890845_2.fastq.gz rna_tumor_fq1=testdata/SRR9134697_1.fastq.gz rna_tumor_fq2=testdata/SRR9134697_2.fastq.gz <br>4 - run the following (this should take about one hour with 16 CPUs)<br>snakemake --printshellcmd --configfile config.yaml --config res=testdata/results_from_fasta prefix=SRR7890830-SRR7890845-SRR9134697 tumor_spec_peptide_fasta=testdata/results_from_fastq/SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta5 - Finally, you will see the SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta and SRR7890830-SRR7890845-SRR9134697_prioritization_from_reads.tsv files in the directory testdata/results_from_fastq. <br>The file SRR7890830-SRR7890845-SRR9134697_prioritization_from_reads.tsv also appears in testdata/results_from_fasta if you prioritized with tumor_spec_peptide_fasta as input. <br><br>

本数据源内文件的生成步骤如下：
1. 克隆位于github.com/XuegongLab/neoguider的Git (Git) 仓库，并按照GitHub官方网站上的说明完成安装。
2. 下载并解压登录号为SRR7890830、SRR7890845及SRR9134697的FASTQ (fastq) 格式测序文件，随后将这些fastq文件放置至testdata目录中。
3. 执行如下Snakemake (Snakemake) 工作流命令（使用16核CPU运行时耗时约3小时）；若已手动将本数据源对应的文件拷贝至testdata/results_from_fastq/SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta路径下，则可直接进入下一步：
snakemake --configfile config.yaml --config res=testdata/results_from_fastq/ prefix=SRR7890830-SRR7890845-SRR9134697 dna_tumor_fq1=testdata/SRR7890830_1.fastq.gz dna_tumor_fq1=testdata/SRR7890830_2.fastq.gz dna_normal_fq1=testdata/SRR7890845_1.fastq.gz dna_normal_fq2=testdata/SRR7890845_2.fastq.gz rna_tumor_fq1=testdata/SRR9134697_1.fastq.gz rna_tumor_fq2=testdata/SRR9134697_2.fastq.gz
4. 执行如下Snakemake工作流命令（使用16核CPU运行时耗时约1小时）：
snakemake --printshellcmd --configfile config.yaml --config res=testdata/results_from_fasta prefix=SRR7890830-SRR7890845-SRR9134697 tumor_spec_peptide_fasta=testdata/results_from_fastq/SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta
5. 最终，你将在testdata/results_from_fastq目录下得到SRR7890830-SRR7890845-SRR9134697_neo_peps.fasta与SRR7890830-SRR7890845-SRR9134697_prioritization_from_reads.tsv两个文件。若以肿瘤特异性肽FASTA (FASTA) 文件作为输入进行优先级排序，则SRR7890830-SRR7890845-SRR9134697_prioritization_from_reads.tsv文件也会出现在testdata/results_from_fasta目录中。