It seems old Illumina encoding 1.5

So yes some tools requiring the fastqsanger would need grooming.

If you are up to programming you can seriously speed this up by using a 
precalculated transfer or hash table.

That way you do not have to do any calculation but just translate each quality 
line using generic regexp/grep/sed like tools or $seq =~ 
t/STARTSCORES/SANGERSCORES/g in perl.

The wiki table could be an alternative option. You still have to set the upload 
type to fastsanger likely since it will probably sniff the header and see its 
fastq but not 1.8+ encoding.



Good luck!

Alex



________________________________
Van: 泽 蔡 [caizexi...@yahoo.com.cn]
Verzonden: dinsdag 4 december 2012 16:41
To: Bossers, Alex
Cc: galaxy-dev@lists.bx.psu.edu
Onderwerp: 回复: [galaxy-dev] 回复: Speed up the galaxy

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<mailto:n...@bx.psu.edu>>
收件人: 泽 蔡 <caizexi...@yahoo.com.cn<mailto:caizexi...@yahoo.com.cn>>
抄送: "galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>" 
<galaxy-...@bx.psu.edu<mailto: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

> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/





___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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

Reply via email to