Submitting NGS data to ArrayExpress via Aspera

Question

[Meisam]

Hi all

I am submitting multiple FASTQ files to the arrayExpress server. The EBI instructions has provided three main method to do this, as I am a macOS user I am left with two options, either FTP or Aspera. Our institution has closed all FTP connections via firewalls so technically I am only left with Aspera. Using this previous biostar post I have managed to install Aspera. On the array express upload instruction page it has mentioned to use the following command for uploading data to the server:

ascp -P 33001 <yourfile.txt> [e-mail]:<your upload directory>/

I have replaced my file name in the <yourfile.txt> but for the upload directory there is no instruction. How am I supposed to know the name to the directory I need to upload my files to?

P.S. ArrayExpress has a tool called Annotate which is used to annotate your uploaded data before submission. In that, there is a FTP/Aspera file upload tab in which they have put the user directory name in their "FTP server" (e.g. ftp-private-2.ebi.ac.uk/lrk**za/), so I have used the same directory name in the ascp command and it has actually worked (although the aspera connects to another server, fasp.ebi.ac.uk)! the file upload is successful but the problem now is that the file in nowhere to be found. It does not appear in my directory which I can see in Annotate. How can I access these successfully uploaded files in Annotate (if it's even possible).

Thanks for bearing with me, any recommendation would be greatly appreciated!

Meisam

[GenoMax]

the file in nowhere to be found.

It is possible that the file transfer server is write only (which is how drop off servers would likely be set up). That is likely the reason you don't see your files. Annotation is generally provided as a metadata file for SRA. I assume you needed to do something similar with the tool you mentioned above.

Answer 1

[Meisam]

For future reference:

For the directory you can use the FTP directory for Aspera submission ([e-mail]:<the directory name on the FTP pop up>), after submission you have to submit the file names and their md5 hashes in the Annotate, then the files would appear.

[GenoMax]

Thank you for coming back and providing a solution. You can accept this answer (green check mark) to provide closure to this thread.