Downloading files

To download your next gen sequencing data, which is in very large files, often in binary, I recommend using the terminal.

 

You probably want to see if you have wget on your computer. From anywhere on the command line, type

wget -V

If that brings up bash command not found, you’re going to want to go to

http://ftp.gnu.org/gnu/wget/

and scroll down. The most recent is currently 1.17.tar.gz

 

Move the file to where you want the wget folder to live (it doesn’t matter much), open up Terminal and navigate there, as shown in the folder movement primer.

Then do these commands (the $ is just indicative of a separate command; do not copy paste the dollar sign):

$ gunzip < wget-1.17.tar.gz | tar -xv

 

$ cd wget-1.12

 

$ ./configure

 

$ make

 

$ make install

 

To download the next gen sequence, navigate to whatever folder you want to be in,

then type

wget -nd -r -l1 -A.gz <web address in email>

That will download all the files that have an .gz entension, which should be all of the raw sequence data. If this produces an error message like:

Resolving \342\200\223nd… failed: nodename nor servname provided, or not known.

this means that there was probably a copy/paste failure. That is, the flags (the hyphen letter part) was type converted into some other type of dash. Try typing that part manually, and the error should go away.

 

This is what you want for RNA-seq or for fin punches. If doing whole genome mapping, the command will be

wget <webaddress in email>/<barcode>/rawSNP.txt

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