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" <[email protected]>
收件人： 泽 蔡 <[email protected]>
抄送： "[email protected]" <[email protected]>; Nate Coraor
<[email protected]>
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:[email protected]
[mailto:[email protected]] Namens ? ?
Verzonden: dinsdag 4 december 2012 16:08
Aan: Nate Coraor
CC: [email protected]
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 <[email protected]>
收件人：泽蔡<[email protected]>
抄送："[email protected]" <[email protected]>
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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