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For example, if your fastq files are in /home/username/mydata and you have a fastq file called Liver_S2_L001_I1_001.fastq.gz then the full path for that fastq file would be: /home/username/mydata/Liver_S2_L001_I1_001R1.fastq.gz
An example datasheet, with 2 samples (Liver and Kidneys), where each sample has 2 fastq files associated with it, might look something like this:
sample | fastq_1 | fastq_2 |
|---|---|---|
Liver | /home/username/mydata/Liver_L001_R1.fastq.gz | /home/username/mydata/Liver_L001_R1.fastq.gz |
Liver | /home/username/mydata/Liver_L002_R1.fastq.gz | /home/username/mydata/Liver_L002_R1.fastq.gz |
Kidney | /home/username/mydata/Kidney_L001_R1.fastq.gz | /home/username/mydata/Kidney_L001_R1.fastq.gz |
Kidney | /home/username/mydata/Kidney_L001_R1.fastq.gz | /home/username/mydata/Kidney_L001_R1.fastq.gz |
1c. Running scrnaseq as a PBS script
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Open RStudio (you can type it in the Windows search bar)
Create a new R script: ‘File’ → “New File” → “R script”
Save this script where your samples folders are (‘File’ → ‘Save’). These should be on your H or W drive. Save the script file as ‘scrnaseq.R’
In the following sections you will be copying and running the R code into your scrnaseq.R script.
Cell Ranger (and nfcore/scrnaseq) generates a default folder and file output structure. There will be a main folder that contains all the sample subfolders (NOTE: this is where you must save your R script). Each sample folder will have an ‘outs’ subfolder. This ‘outs’ folder contains a ‘filtered_feature_bc_matrix’ folder, which contains the files that Seurat uses in its analysis.
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You can manually set your working directory in RStudio by selecting ‘Session' -> 'Set working directory' -> 'Choose directory'. Choose the same directory as you saved your scrnaseq.R script, previous section. This will output the setwd(...) command with your working directory into the console window (bottom left panel). Copy this command to replace the default setwd(...) line in your R script.
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