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2571cf0 · Aug 22, 2024

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  1. https://github.com/hermanzhaozzzz/snakepipes_fastqc-multiqc 先跑质控流程,主要是看看需不需要trim 5‘ 端的不稳定序列和3'端质量不够高的reads
  2. 跑mapping流程,如果是star mapping,就用这个流程即可
  3. 执行Snakefile进行 cutadapt、Star mapping、bam sort等处理
  4. 后续1,可以选择GATK SNP calling和差异表达分析
  5. 后续2,差异表达基因
    • 可以使用Snakefile.fc.deseq2.py计算差异表达基因的featureCounts
    • 并且使用format_all.featureCounts.form.ipynb整理表格数据
    • 最后使用DESeq2_plots.ipynb绘图

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