Hi Brad, Galaxy Support- Besides changing them individually, is there a way to modify the settings for a large number files from fastq to fastqsanger in batch? Either via the bioblend or manually via the UI?
Thanks, Dave On Fri, Dec 7, 2012 at 3:53 AM, Langhorst, Brad <langho...@neb.com> wrote: > 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: 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/ > > > -- > 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/ >
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