Hi Yan,

I also had problems with NBIC FTP.
NBIC allows only 10 GB space for user.
I made my BAM files in main server (using Tophat2) and then uploaded them to NBIC using their download URLs.
It was fast. It took me less than a hour to move 16 BAM files (around 9.5 GB).
You may try this.
Good luck.

Best wishes,
Anto


From: Yan He [yanhe83@hotmail.com]
Sent: 22 August 2013 09:36
To: Anto Praveen Rajkumar Rajamani; galaxy-user@lists.bx.psu.edu
Subject: 答复: [galaxy-user] Counts of mapped reads for each gene?

Hi Anto,

Thank you very much for your reply! I tried Galaxy/NBIC. However, I had problem with uploading my files. I used FTP, because the file I had was larger than 2G, but I couldn’t connect to the NBIC FTP. Do you have some idea how to solve the problem? Thanks!

Yan

 

发件人: Anto Praveen Rajkumar Rajamani [mailto:APR@hum-gen.au.dk]
发送时间: Thursday, August 22, 2013 3:14 PM
收件人: Yan He; galaxy-user@lists.bx.psu.edu
主题: RE: [galaxy-user] Counts of mapped reads for each gene?

 

Hi Yan,

 

You may use the HTseq count wrapper in the http://galaxy.nbic.nl/.

It does a good job and I could employ edgeR on that count matrix.

Good luck.

 

Best wishes,

Anto