GRAND-SLAM analysis of SARS-CoV-2 data from Finkel et al., Nature 2021 (https://www.nature.com/articles/s41586-021-03610-3)
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This is the processed SLAM-seq data from Finkel et al., Nature 2021 (https://www.nature.com/articles/s41586-021-03610-3). The zip file contains the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output). The json file is required if you want to start from scratch. The file sars.tsv.gz is the GRAND-SLAM output table. To generate the GRAND-SLAM output yourself, first prepare the human (ensembl v90) and the SARS-CoV-2 genome (NC_045512). Then run: gedi -e Slam -trim5p 15 -reads sars.cit -genomic h.ens90 SARS-CoV2 -prefix grandslam_t15/sars -plot -progress To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it. You can also start from scratch (i.e., the json file): Prepare the human genome (ensembl v90), the SARS-CoV-2 genome (NC_045512), the human rRNA sequence (U13369.1), and the Mycoplasma hominis sequence Prepare the joint STAR index for the human and virus genome by calling gedi -e GenomicUtils -p -m star -g h.ens90 SARS-CoV2 Modify the starindex entry in the json file to match your file system Run: gedi -e Pipeline -r parallel -j sars.json rnaseq_mapping.sh report.sh grandslam.sh Software versions: gedi toolkit 1.0.4 GRAND-SLAM 2.0.7 cutadapt 3.4 Bowtie 2 version 2.3.0 STAR version 2.5.3a
本数据集源自Finkel等人2021年发表于《自然》（Nature）的研究（https://www.nature.com/articles/s41586-021-03610-3）的经处理SLAM-seq数据。该压缩包包含分析处理流程的完整输出结果，涵盖比对读数、流程运行脚本及最终处理输出文件。若需从头启动完整分析流程，需使用配套的JSON文件。其中sars.tsv.gz为GRAND-SLAM输出表格。 若需自行生成GRAND-SLAM输出，请先准备人类参考基因组（Ensembl v90）及SARS-CoV-2基因组（NC_045512），随后执行以下命令： gedi -e Slam -trim5p 15 -reads sars.cit -genomic h.ens90 SARS-CoV2 -prefix grandslam_t15/sars -plot -progress 若需生成cit格式文件，请修改start.bash的首行内容以匹配您本地文件系统的路径，随后运行该脚本。您也可选择从头构建完整分析（即基于JSON文件）：需先准备人类参考基因组（Ensembl v90）、SARS-CoV-2基因组（NC_045512）、人类核糖体RNA序列（U13369.1）以及人型支原体（Mycoplasma hominis）序列。 通过执行命令gedi -e GenomicUtils -p -m star -g h.ens90 SARS-CoV2，为人类与病毒基因组构建联合STAR索引。 修改JSON文件中的starindex条目以匹配您本地的文件系统路径，随后执行以下命令： gedi -e Pipeline -r parallel -j sars.json rnaseq_mapping.sh report.sh grandslam.sh 所用软件版本如下：gedi toolkit 1.0.4、GRAND-SLAM 2.0.7、cutadapt 3.4、Bowtie 2 2.3.0、STAR 2.5.3a
