Hello Teresita,
Yes, the tool is at the public server under "NGS: SAM Tools -> rmdup remove PCR duplicates". Instructions for use are in the tool form under "What it does".
An uploaded BAM file (only upload the .bam, not the index .bam.bai, Galaxy creates that new) will appear on the "Get Data -> Upload File" tool form, in section "Files uploaded via FTP:". From there, check the file(s) and move into a history. Exact instructions, including a screencast, are in the Galaxy wiki: http://wiki.g2.bx.psu.edu/FTPUpload
Your FTP client (unix or desktop) will provide information about the status of a transfer. There is a 50G size limit on individual files. Files loaded successfully need to be moved from the "Upload File" transfer area to a history within 3 days (after that they are purged).
Hopefully this helps, but please provide more details if you are still having problems,
Jen Galaxy team
On 4/25/12 10:57 AM, Teresita Diaz De Ståhl wrote:
Hello
I wonder if it is possible to rmdupl using galaxy on the free public server.
I uploaded the bam files via ftp (main.g2.bx.psu.edu) but they are not visible in my public interface, I can only see the fastq uploaded files.
I would very much appreciate some suggestion how to remove PCR duplicates from my bam files
Thanks
Teresita
*Teresita Díaz de Ståhl,***
*Department of Oncology-Pathology*
*Cancer Center Karolinska, CCK R8:04*
*Karolinska Institutet*
*SE-171 76 Stockholm, Sweden*
*+46-8-517 721 35 (office)*
*E-mail: Teresita.Diaz.de.Stahl@ki.se mailto:Teresita.Diaz.de.Stahl@ki.se***
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: