Hi Brad-

In the past, I had always been running the time-consuming fastqgroomer
step. However, based on this thread, I now realize this step is sometimes
unnecessary.

Here is my question. I have a large number of fastq data files that are
already in data libaries. They were imported in "fastq" format. I was
trying to figure out if there is an easy way to change the metadata to
"fastqsanger" in batch, without having to do it manually, file by file.

One approach is to recreate another library -- and reimport them with the
correct "fastqsanger" format selected.

However, I was trying to see if there was an existing feature that allows
me to select a bunch of files and then edit the metadata.

Thanks,
Dave



On Thu, Apr 25, 2013 at 1:58 AM, Langhorst, Brad <langho...@neb.com> wrote:

>  Hi dave:
>
>  The fastq groomer tool will convert your fastq files (of unknown base
> quality scale) to fastqsanger.  Are you sure these files are not already
> sanger scaled? Modern illumina pipelines produce fastqsanger files.
>
>  If you do know the scale, just import the files explictly as fastqsanger
> (not fastq).
>
>  Galaxy team - maybe the sniffer should be smarter about guessing the
> file format…
>
>  If you need to convert a large number you could set up a galaxy workflow
> with a single fastq groomer step.  That would allow you to start the job on
> many fastq files at once.
>
>
>
>  Brad
>
>  On Apr 25, 2013, at 12:14 AM, Dave Lin <d...@verdematics.com> wrote:
>
>  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
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>> >
>> >  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
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>>
>>  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/
>>
>
>
>   --
> Brad Langhorst
> langho...@neb.com
>
>
>
>
>
>
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