Hi Alex
 
I look the page of wikipedia, but I have a little confused. We sequenced with 
solexa. I paste a read of my data, can you tell me whether I need run Groom?
The read is like this:@HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1
AGAAGTACATCGCGATGCCGTTNCCNNCGAAGGCGATAGNNNACAAGNCCAAATGNTTCTNCATCNNNCNCGAGNNGNCGAGGNCGCCGTGCGACCCTGC
+HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1
Ya^a`edddeddc\c`a`dc]\Ba^BBZ]ZZ`ZZZ]a]]BBB^[`\UB_V[V\`ZBSZX^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 

________________________________
 发件人: "Bossers, Alex" <alex.boss...@wur.nl>
收件人: 泽 蔡 <caizexi...@yahoo.com.cn> 
抄送: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>; Nate Coraor 
<n...@bx.psu.edu> 
发送日期: 2012年12月4日, 星期二, 下午 11:21
主题: RE: [galaxy-dev] 回复:  Speed up the galaxy
  

 
Hi 
  
I presume the best way to optimise your current problem is to evaluate whether 
you really need to groom your data!? If its old data presumably yes, but if it 
is recent data in Illumina 1.8+ 
encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary.... 
speedup 100% :-) 
Groom would take long at our servers as well but due to the new Illumina format 
we didn’t bother to optimise it further by parallelisation for instance... 
  
Alex 
  
  
Van:galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens ? ?
Verzonden: dinsdag 4 december 2012 16:08
Aan: Nate Coraor
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] 回复:Speed up the galaxy   
  
Hi,  
   
I read the page of the document. But I don't think there is anything I 
need. Now, I installed a local instance of galaxy, and I just run it on a PC. I 
need to deal with large data, if I just use the default configure of galaxy, 
every task would take long time. For example I ran the FASTQ Groomer with a 
large file, the precedure is so slow, and galaxy would not use the potential of 
my machine. So I want to know how can I get galaxy ran faster. I already can 
upload files quickly and I just need to know how to ran tools quickly.  
发件人:Nate Coraor <n...@bx.psu.edu>
收件人:泽蔡<caizexi...@yahoo.com.cn> 
抄送:"galaxy-...@bx.psu.edu" <galaxy-...@bx.psu.edu> 
发送日期:2012年12月4日, 星期二, 下午9:38
主题:Re: [galaxy-dev] Speed up the galaxy  

On Dec 4, 2012, at 4:36 AM, 泽蔡wrote:

> Hi all,
>  
> How can I speed up the galaxy? Like how to use more cores and memeries.

Hi,

This is a pretty broad question.  However, I would recommend that you start at:

    http://usegalaxy.org/production

--nate

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