[galaxy-dev] 回复： 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^ 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 ___ 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/
Re: [galaxy-dev] 回复： 回复： Speed up the galaxy
Hi, You can use fastQC to find out what is the quality encoding of your sequences http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Alternatively, you can also use this script: http://www.uppmax.uu.se/userscript/check-fastq-quality-score-format David Date: Tue, 4 Dec 2012 23:41:27 +0800 From: caizexi...@yahoo.com.cn To: alex.boss...@wur.nl CC: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] 回复： 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^ 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 ___ 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/___ 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/
Re: [galaxy-dev] 回复： 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: 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^ 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.edumailto:n...@bx.psu.edu 收件人： 泽 蔡 caizexi...@yahoo.com.cnmailto:caizexi...@yahoo.com.cn 抄送： galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu galaxy-...@bx.psu.edumailto: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/
