transfer example VCF to tcga

[GoogleCodeExporter]

Moiz,

Jia mentioned that we use an "other" directory at DCC for uploads.  If you know 
how to access this directory, would it be possible for you to copy the 
following 9 GB file there for us?

/export/uec-gs1/laird/shared/production/ga/merges/2013-03-06_1323_merge_NIC1254A
15/results/MERGING/MERGING_1_NIC1254A15/ResultCount_MERGING_1_NIC1254A15.hg19_rC
RSchrm.fa.realign.mdups.recal.cpg.filtered.sort.vcf

Thanks,
Ben.

---------- Forwarded message ----------
From: Liu, Jia (NIH/NCI) [C] <jia.liu3@nih.gov>
Date: Thu, Jul 25, 2013 at 12:30 PM
Subject: Re: question about bisulfite sequencing data
...
For FTP upload, Todd mentioned that you an use your "other" directory in the 
normal sftp location. We have read access so we can get files left there. 
Please let us know if you have any questions about this.
---------- End Forwarded message ----------

Original issue reported on code.google.com by benb...@gmail.com on 31 Jul 2013 at 8:14

[GoogleCodeExporter]

Hi Ben,

That directory is for array data upload. Do you have access to the TCGA sftp 
uploads directory? Did Jia mean the directory that we use for array data or did 
she mean a specific directory where you will be uploading your Level 3 data? If 
it's the same directory that I upload data to then I can upload your file. 

Let me know how you want me to proceed.

Thanks,

Moiz

Original comment by msbootwa...@gmail.com on 31 Jul 2013 at 8:22

[GoogleCodeExporter]

See her email above.  I believe she just meant whatever we have been using for 
array, since I don't think we've uploaded any sequence data yet.  I would just 
go ahead and upload it to the array "other" directory.  If you're able to 
easily change the destination filename, we could make it something super clear 
like "EXAMPLE_WGBS_LEVEL2_DATA.vcf".

Could you let Jia know when the transfer is complete?

Thanks,
Ben.

Original comment by benb...@gmail.com on 31 Jul 2013 at 8:30

[GoogleCodeExporter]

Original comment by zack...@gmail.com on 31 Jul 2013 at 8:31

• Changed title: transfer example VCF to tcga

[GoogleCodeExporter]

Started upload. Will update once upload is completed.

Original comment by msbootwa...@gmail.com on 31 Jul 2013 at 8:52

[GoogleCodeExporter]

Upload complete. The file has been uploaded to the TCGA sftp site in the 
following directory: /gccusc/other/WGBS and is named 
EXAMPLE_WGBS_LEVEL2_DATA.vcf

Original comment by msbootwa...@gmail.com on 31 Jul 2013 at 9:42

[GoogleCodeExporter]

The change for this is done now.

Original comment by msbootwa...@gmail.com on 31 Jul 2013 at 9:50

• Changed state: Fixed