Hi Brad, I'm sorry, I can not quite follow you. The "pencil" and the "datatype tab" are tools in galaxy?
________________________________ 发件人： "Langhorst, Brad" <langho...@neb.com> 收件人： 泽 蔡 <caizexi...@yahoo.com.cn> 抄送： "galaxy-dev@lists.bx.psu.edu Dev" <galaxy-dev@lists.bx.psu.edu> 发送日期： 2012年12月7日, 星期五, 7:53 下午 主题: Re: [galaxy-dev] 回复： 回复： 回复： Speed up the galaxy You can just change the format of the data from fastq to fastqsanger if you're sure about the error format (use the pencil, then datatype tab) note: fastqsanger !=fastqcsanger Brad On Dec 7, 2012, at 3:20 AM, 泽 蔡 <caizexi...@yahoo.com.cn> wrote: Hi Alex > >Now is an another problem. I now deal with two fastq files, there are Illumina >enconding 1.8 and pair-end, so I don't need to groom. But the fact is, I need >to use the "filter by quality" and "Fastq interlacer" and without groom thses >two tools can not regonize the files. Any idea to solve this problem? > > > >________________________________ > 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> >发送日期： 2012年12月5日, 星期三, 4:02 上午 >主题: RE: 回复： [galaxy-dev] 回复： Speed up the galaxy > >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: mailto: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: mailto: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: mailto: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/ -- Brad Langhorst langho...@neb.com
___________________________________________________________ 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/
