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update the output dirs
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malachig committed Jun 19, 2024
1 parent 4c4d542 commit 325ce34
Showing 1 changed file with 3 additions and 12 deletions.
15 changes: 3 additions & 12 deletions _posts/0003-04-03-DE_Visualization_AdvancedR.md
Original file line number Diff line number Diff line change
@@ -33,7 +33,9 @@ Expression and differential expression files will be read into R. The R analysis
Start RStudio, or launch a posit Cloud session, or if you are using AWS, navigate to the correct directory and then launch R:

```bash
cd $RNA_HOME/de/ballgown/ref_only/
mkdir $RNA_HOME/de/visualization_advanced
cd $RNA_HOME/de/visualization_advanced

R
```

@@ -46,16 +48,6 @@ library(gplots)
library(GenomicRanges)
library(ggrepel)

#Set working directory where results files exist
datadir = "~/workspace/rnaseq/de/ballgown/ref_only"
outdir = "~/workspace/rnaseq/de/manual_viz"
if (!dir.exists(outdir)) dir.create(outdir)

setwd(datadir)

# List the current contents of this directory
dir()

#Import expression results (TPM values) from the HISAT2/Stringtie pipeline (http://genomedata.org/rnaseq-tutorial/results/cshl2022/rnaseq/gene_tpm_all_samples.tsv)
gene_expression = read.table("~/workspace/rnaseq/expression/stringtie/ref_only/gene_tpm_all_samples.tsv", header = TRUE, stringsAsFactors = FALSE, row.names = 1)

@@ -64,7 +56,6 @@ gene_names=read.table("~/workspace/rnaseq/de/htseq_counts/ENSG_ID2Name.txt", hea
colnames(gene_names) = c("gene_id", "gene_name")

#Import DE results from the HISAT2/htseq-count/DESeq2 pipeline (http://genomedata.org/cri-workshop/deseq2/DE_all_genes_DESeq2.tsv)
setwd(outdir)
results_genes = read.table("~/workspace/rnaseq/de/deseq2/DE_all_genes_DESeq2.tsv", sep = "\t", header = TRUE, stringsAsFactors = FALSE)

```

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