Changes between Version 6 and Version 7 of SOPs/submittingSequencingToGEO


Ignore:
Timestamp:
01/07/26 16:26:45 (2 months ago)
Author:
kdesilva
Comment:

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  • SOPs/submittingSequencingToGEO

    v6 v7  
    24241. Send this information to the BaRC person who is helping you.[[br]] [[br]]
    2525
    26 After the BaRC person has finished uploading your data to GEO, they will let you know.
    27 
    28 1. Go back to GEO, log in, and go to https://submit.ncbi.nlm.nih.gov/geo/submission/  [[br]] [[br]]
    29 1. Let NCBI know that your FTP file transfer to GEO is complete.   [[br]] [[br]]
    30 1. NCBI will let you and BaRC know when your private-for-now GEO web pages are available.  [[br]] [[br]]
    31 1. Check that the sample descriptions are clear and complete.  [[br]] [[br]]
    32 1. Right before or after your publication is made public, change the GEO access from private to public.  [[br]] [[br]]
    33 
    3426To upload your files to GEO, you can use a file transfer program with a graphical interface (as recommended by GEO), or you can use a command-line method on a Whitehead server.  Two options are ftp and ncftp.  In the simplest case, all of your files for submission will be in the same directory.  Start by going to that directory on the WI server and then confirm that the files are actually there.
    3527
    … …  
    4638ftp ftp-private.ncbi.nlm.nih.gov
    4739# You'll be prompted for your username and password
     40#You can find the login credentials at https://www.ncbi.nlm.nih.gov/geo/info/submissionftp.html
     41#These credentials are changed regularly, as per GEO security policies.
    4842name: geoftp
    49 password: MYPASSWD  # each submission is different
     43password: MYPASSWD # each submission is different
    5044# Now you should be connected to the GEO server.  Change to the directory you were given
    5145cd uploads/jsmith_e123ABC
    … …  
    7569
    7670When the file upload is complete, follow through by submitting your metadata file to GEO (according to the instructions on their website).
     71
     72
     73After the BaRC person has finished uploading your data to GEO, they will let you know.
     74
     751. Go back to GEO, log in, and go to https://submit.ncbi.nlm.nih.gov/geo/submission/  [[br]] [[br]]
     761. Let NCBI know that your FTP file transfer to GEO is complete.   [[br]] [[br]]
     771. NCBI will let you and BaRC know when your private-for-now GEO web pages are available.  [[br]] [[br]]
     781. Check that the sample descriptions are clear and complete.  [[br]] [[br]]
     791. Right before or after your publication is made public, change the GEO access from private to public.  [[br]] [[br]]
     80