表达分析脚本差异

# 差异表达分析
mkdir -p /home/train/08.RNA-seq_analysis_by_trinity/diff_exp
cd /home/train/08.RNA-seq_analysis_by_trinity/diff_exp
ln -s ../exp_cal/out.gene_rawCounts.matrix gene.rawCount.matrix
ln -s ../exp_cal/out.gene_TPM.not_cross.matrix gene.TPM.not_cross.matrix
/opt/biosoft/Trinity-v2.11.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix gene.TPM.not_cross.matrix > gene.TPM.TMM.matrix

echo -e "S4\tA
S4\tB
S4\tC
S2\tD
S2\tE
S2\tF
S2\tG" > samples.txt
# 对两两样本counts总和 >= 40 的基因进行差异表达分析
#/opt/biosoft/trinityrnaseq-Trinity-v2.1.1/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix genes.counts.matrix --method edgeR --samples_file samples.txt --min_rowSum_counts 40 --output edgeR.genes.dir
/opt/biosoft/Trinity-v2.11.0/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix gene.rawCount.matrix --method edgeR --samples_file samples.txt --output edgeR.genes.dir

cd edgeR.genes.dir
# 提取差异表达基因进行聚类分析和热图制作
/opt/biosoft/Trinity-v2.11.0/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../gene.TPM.TMM.matrix -P 0.001 -C 2 --samples ../samples.txt
#/opt/biosoft/Trinity-v2.11.0/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../gene.TPM.TMM.matrix -P 0.01 -C 1 --samples ../samples.txt --order_columns_by_samples_file