You will need the following data files to run the DADA2 pipeline:
Raw barcodes file from entire run (may need to be manipulated before DADA2)
Index run: Undetermined_S0_L001_I1_001.fastq
Read 1: Undetermined_S0_L001_R1_001.fastq
Read 2: Undetermined_S0_L001_R2_001.fastq
If you are just learning how to copy files from a remote server to your home computer, here is a step by step guide for using a CU Boulder lab server. There are many ways of doing this; here is one example:
Step 1. If you are multiple downloading runs with different primers, make sure to create separate folders for each of the runs (i.e. 16S, 18S, and ITS should all have different folders). This is important because the files are named the same regardless of the runs, they will be overwritten if not put in separate folders. The script below relies on folders being added to the Desktop named 16S, 18S, and ITS as an example.
Step 2. If you are remote, connect to the VPN. I connect through the Cisco app set up by our department's IT administrator.
Step 3. Find file paths of files you want to download (skip if you know file paths already)
a. Open Terminal Window and connect to the remote server.
type ssh [user]@[IP address for server]
example: ssh kim@123.789.678.567 (this IP address is made up.)
b. Move up directories two levels; i.e. type "cd .." press enter and then repeat "cd ..".
c. Navigate to sequencing runs... e.g. med/LabData/seq_runs/miseq_
d. I find it helpful to paste the file paths in a text editor for the following steps.
Again these are the four files you will need:
Raw barcodes file from entire run (may need to manipulate before DADA2)
Index run: Undetermined_S0_L001_I1_001.fastq
Read 1: Undetermined_S0_L001_R1_001.fastq
Read 2: Undetermined_S0_L001_R2_001.fastq
Step 4. Now you can copy the four files above from the server to your personal computer. Tip: if you copy the raw barcodes file, you can manipulate the file while the other files are downloading (they are large and take a while).
a. Open a new Terminal window from your home/ personal computer.
i. From Terminal headers, Shell -> New Terminal Window
b.
Type the command scp (secure copy), space, the address from the files on the server, space, and finally the path of the directory to store the files on your personal computer. The star at the end of the truncated file name indicates it will download any file including the name up until that point.
16S
scp USERNAME@SERVER:/file/path/for16S/barcodes.txt File/path/name/16S
scp USERNAME@SERVER:/file/path/for16S/Undetermined_S0_L001_* Desktop/16S
18S
scp USERNAME@SERVER:/file/path/for18S/barcodes.txt File/path/name/18S
scp USERNAME@SERVER:/file/path/for18S/Undetermined_S0_L001_* Desktop/18S
ITS
scp USERNAME@SERVER:/file/path/forITS/barcodes.txt File/path/name/ITS
scp USERNAME@SERVER:/file/path/forITS/Undetermined_S0_L001_* Desktop/ITS
Using the example above, you would now have all three files for each of the three different runs 16S, 18S, and ITS in folders named 16S, 18S, and ITS.
Now you need to prepare the barcode file for your particular project. See instructions here!
Comentários