Are you sure you nee to interlace? If you align using bowtie you specify two files of fastq data (one for read 1 and one for read2)

I don't know how the interlacer works, but some tools depend on being able to parse the read names to understand which reads go together - it is possible that the interlacer may not understand this read name format.

Brad On Dec 7, 2012, at 8:31 AM, 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> wrote:

Hi Brad,

I know and I tried, but the "filter by quality" report an error and the "Fastq interlacer" still treat the pair-end reads as two unrelated reads. I paste one line of my data, the right-hand of pair-end read. @HWI-ST1106:232:D14FHACXX:6:1101:1131:2250 2:N:0:GCCAAT CACCTAAAACTCCTATGCACTCNNCATAAACTTACAATAGATCAACTTCATCCACTAGCCTTGAGCCAAACTAATAAAACAGTGCCACGAGCCCGAAAGT + @@BFFFDFFFHFHIIGIIJJJJ##3<CFCGGGCHEHGICGEGAHICGEIGFC>GHHGIGGJJIG@HGII@GGIGHDEEA@BE@C<CCC?BDD=?B6<@>D Can you have any idea that at least I can use the "Fastq interlacer"? 发件人： "Langhorst, Brad" <Langhorst@neb.commailto:Langhorst@neb.com> 收件人： 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> 抄送： "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> 发送日期： 2012年12月7日, 星期五, 8:40 下午 主题: Re: 回复： [galaxy-dev] 回复： 回复： 回复： Speed up the galaxy

<PastedGraphic-2.png> see that pencil icon - that lets you change the settings for a given dataset.

then you'll see a datatype tab

Brad On Dec 7, 2012, at 7:23 AM, 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> wrote:

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" <Langhorst@neb.commailto:Langhorst@neb.com> 收件人： 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> 抄送： "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev" <galaxy-dev@lists.bx.psu.edumailto: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 <caizexi123@yahoo.com.cnmailto:caizexi123@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.Bossers@wur.nlmailto:Alex.Bossers@wur.nl> 收件人： 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> 抄送： "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto: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 [caizexi123@yahoo.com.cnmailto:caizexi123@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.Bossers@wur.nlmailto:Alex.Bossers@wur.nl> 收件人： 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn> 抄送： "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu>; Nate Coraor <nate@bx.psu.edumailto:nate@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@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 <nate@bx.psu.edumailto:nate@bx.psu.edu<mailto:nate@bx.psu.edumailto:nate@bx.psu.edu>> 收件人： 泽 蔡 <caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn<mailto:caizexi123@yahoo.com.cnmailto:caizexi123@yahoo.com.cn>> 抄送： "galaxy-dev@bx.psu.edumailto:galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edumailto:galaxy-dev@bx.psu.edu>" <galaxy-dev@bx.psu.edumailto:galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edumailto:galaxy-dev@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 langhorst@neb.commailto:langhorst@neb.com

-- Brad Langhorst langhorst@neb.commailto:langhorst@neb.com

-- Brad Langhorst langhorst@neb.commailto:langhorst@neb.com