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Bioinformatics:Download data

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Aspera

Copy the aspera install script to your home directory

cp /scratch/helpdesk/ngs/aspera-connect-3.6.2.117442-linux-64.sh ~/

Run the script from your home directory. This will install configuration files in ~/.aspera

cd ~/
./aspera-connect-3.6.2.117442-linux-64.sh


Downloading 1000 genomes data

Login to an Ada fast transfer node from your desktop

ssh NetID@ada-ftn1.tamu.edu

Sample command to download a fastq.gz file

~/.aspera/connect/bin/ascp -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -QTr -l10000m \
anonftp@ftp-trace.ncbi.nih.gov:/1000genomes/ftp/phase3/data/NA21087/sequence_read/SRR442587_1.filt.fastq.gz ./


Uploading to SRA

Login to an Ada fast transfer node from your desktop

ssh NetID@ada-ftn1.tamu.edu

Sample command to upload to SRA

~/.aspera/connect/bin/ascp -i <path/to/ncbi_key_file> -QT -l10000m -k1 -d \
<path/to/files/directory/> subasp@upload.ncbi.nlm.nih.gov:uploads/NCBI_account_email_<random_code>/<submission_folder>/

<path/to/key_file> key file is provided by NCBI. must be an absolute path, e.g.: $HOME/keys/aspera.openssh

<random_code> random code for upload is provided by NCBI

<submission_folder> is required and will be created automatically by the ascp command.