Hello,

On 4/28/11 9:21 PM, puvan...@umn.edu wrote:
I am new to Galaxy and I am not sure whether these topics were discussed
earlier. I followed the steps up to cufflinks and I did not have any
problems. Thanks for the RNA seq tutorial. My questions are
1. How do I know the number of reads mapped against the reference genome
used after Top Hat mapping


Please try: "NGS: SAM Tools -> flagstat provides simple stats on BAM files"

2. I am aware that Cuffdiff is used to find the differences in
expression. How do I combine replicates (3) of different treatments ?

Set the "NGS: RNA Analysis -> Cuffdiff" form so that the second choice, "Perform replicate analysis:" is "Yes". The ability to add/define groups from your history will pop up when the form modifies in response to this selection.

Best wishes for your research,

Jen
Galaxy team




SP
___________________________________________________________
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:

http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
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:

 http://lists.bx.psu.edu/

Reply via email to