Pub-Script/0_raw/step.sh
2025-06-01 21:09:16 +08:00

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###从NCBI下载基因组(DNA)/转录组(RNA)测序数据到获得预测基因的处理步骤以Nyctotherus_ovalis物种为例见/home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA。如果没有注明仅基因组数据要做其他步骤基因组和转录组步骤一样。直接写在本文件里的美丽表示可以直接终端运行指令其他指令要提交pbs任务运行。
screen -S ncbi_dl #screen命令创建一个新的窗口这里窗口命名为ncbi_dl用来下载原始测序数据
wget -c -b -i species_name_urls.txt #NCBI下载每个物种相应所有原始数据至服务器species_name_urls.txt包括SRA数据的urls链接
#命令运行成功后按下组合键ctrl+A+D退出当前窗口
screen -r ncbi_dl #返回ncbi_dl窗口查看下载进度
:fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files SRR10355986.1 #RNA数据转换数据格式为左右两端read文件
:fastq-dump --split-files SRR10355986.1 #DNA数据转换数据格式为左右两端read文件