Navigate to directory with your results
- Check size of files and directories, and think about what you'd like to save
- Don't need original data (we have that for you on the course website), software tools (can be downloaded)
cd ~/workspace/rnaseq/integrated_assignment
du -sh *
This shows size of all files and directories in the integrated assignment folder
- hisat2 directory is very big--probably don't need to save this because we can recreate the indexes from the original data
Best to compress files into one folder for transferring (quicker, more organized)
- Make a directory to store the files you want to copy over
mkdir rna-backup
- Move files into this directory
- List everything you want to move, and the last item in the list is where the files will be moved
- Use regex to grab similarly named files (
*)
mv Normal* Tumor* adapter ballgown expression multqc_report.html trimmed_reads rna-backup
Compress the folder that will be copied to your computer
- name of compressed file, followed by what you are compressing (can be multiple files/directories)
tar -vczf rna-backup.tar.gz rna-backup
Navigate to the directory with your AWS permisions key (CBWNY.pem for mac or linux, CBWNY.ppk for windows)
- Copy over using your student number instead of
## - Need to specify permissions key
- Dot at the end means copy the data in the current directory
rsync -azv -e "ssh -i CBWNY.pem" ubuntu@##.oicrcbw.ca:/home/ubuntu/workspace/rnaseq/integrated_assignment/rna-backup.tar.gz .
You can also use scp, which is a bit simpler, but often not as fast
scp -i CBWNY.pem ubuntu@##.oicrcbw.ca:/home/ubuntu/workspace/rnaseq/integrated_assignment/rna-backup.tar.gz .