Often, researchers will need to submit their experimental data to the NCBI database Gene Expression Omnibus (GEO) prior to a publication or at the completion of a study. GEO accepts data from such methods as ChIP-seq, RNA-seq, and bisulfite sequencing, among many other types.
This page is a guide to transferring your data, that is stored on the O2 cluster, to NCBI's FTP server. Please note that this page is not a replacement for the submission instructions provided by GEO; it is a supplement that clarifies how to perform the transfer process using HMS RC resources.
Here is a description of the transfer and submission preparation process:
md5sum
command on the O2 cluster.transfer.rc.hms.harvard.edu
lftp
to connect to the NCBI FTP server. To obtain the appropriate lftp
command, log into GEO and navigate to this page. The command will be listed under "Uploading your submission" > "FTP instructions" > "Linux/Unix" > "Here is a typical 'lftp' session". The command will be in the form of: lftp ftp://username:password@server
mirror -R GEOusername_directory
If you have any difficulty following these instructions, feel free to contact us!