diff --git a/_episodes/rnaseq_BLAST.md b/_episodes/rnaseq_BLAST.md index 8f927c4..e5ee2ff 100644 --- a/_episodes/rnaseq_BLAST.md +++ b/_episodes/rnaseq_BLAST.md @@ -513,10 +513,6 @@ cd Venn cut -f 1 ../DEG/DESeq2.#####.dir/RSEM.isoform.counts.matrix.DT_vs_WT.DESeq2.DE_results.P0.001_C1.DT-UP.subset | grep -v sample > DESeq.UP.subset cut -f 1 ../DEG/DESeq2.####.dir/RSEM.isoform.counts.matrix.DT_vs_WT.DESeq2.DE_results.P0.001_C1.WT-UP.subset | grep -v sample > DESeq.DOWN.subset -###edgeR -cut -f 1 ../DEG/edgeR.####.dir/RSEM.isoform.counts.matrix.DT_vs_WT.edgeR.DE_results.P0.001_C1.DT-UP.subset | grep -v sample > edgeR.UP.subset -cut -f 1 ../DEG/edgeR.####.dir/RSEM.isoform.counts.matrix.DT_vs_WT.edgeR.DE_results.P0.001_C1.WT-UP.subset | grep -v sample > edgeR.DOWN.subset - ``` ```bash ## IF YOU ARE NOT IN BASE ENVIRONMENT @@ -526,8 +522,8 @@ conda activate venn pip install --upgrade numpy pandas ### Drawing -intervene venn -i DESeq.DOWN.subset DESeq.UP.subset edgeR.DOWN.subset edgeR.UP.subset --type list --save-overlaps -intervene upset -i DESeq.DOWN.subset DESeq.UP.subset edgeR.DOWN.subset edgeR.UP.subset --type list --save-overlaps +intervene venn -i DESeq.DOWN.subset DESeq.UP.subset --type list --save-overlaps +intervene upset -i DESeq.DOWN.subset DESeq.UP.subset --type list --save-overlaps ``` ### Assignment