Re: [galaxy-dev] automatic adding of a tab in a fastq header
Hi Peter,
I tested it on the last version of the dev and master branches.
step-by-step :
I click on the "shared data/Data Libraries", I select my library and I
click on the button to upload a file and I select the option "from User
Directory". I select my fastqsanger file (sequences headers are like this :
@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC
with a space between @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and
1:N:0:ATGAGC and I import it (with or without the auto-detect option).
When I look the file in a history, the space between
@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
replaced by a tab.
I didn't have this problem with "shared data/ Data Libraries deprecated".
Thank a lot for your help,
Best,
Fabien
On 18/03/2016 18:59, Peter Cock wrote:
Can you provide more details - in particular the version of Galaxy
you
are running? A step-by-step description of how you did the data import
might be useful too for the Galaxy team to try to reproduce this.
Peter
On Fri, Mar 18, 2016 at 5:34 PM, Fabien Mareuil <fmareuil(a)pasteur.fr> wrote:
> Hi Peter,
>
> Thank a lot for this information, I didn't found this option for the new
> version of the Data Libraries.
> This could explain why there is this conversion.
> I tested it with an automatic format detection and when I set explicitly the
> format but in the two cases a tab was added.
>
> Fabien
>
>
> Le 18/03/2016 17:04, Peter Cock a écrit :
>> Hi Fabien,
>>
>> There is a Galaxy upload option to turn spaces into tabs, useful for
>> tables of data. Is that being ticked by mistake? That would explain
>> this problem.
>>
>> Also I would check if the FASTQ file format is being detected
>> automatically, or set explicitly (e.g. fastqsanger)? Doing that ought
>> to prevent any changes.
>>
>> Peter
>>
>> On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil <fmareuil(a)pasteur.fr>
>> wrote:
>>> Hi,
>>>
>>> We got a problem with the new version of Data libraries. When we upload a
>>> fastq file from a User Directory, a tabulation character is added in the
>>> header in replacement of a space character.
>>>
>>> from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to
>>> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC
>>>
>>>
>>> This behavior causes an error with cutadapt 1.6 (maybe with other tools)
>>> because it doesn't work with tab character. With the direct upload tool
>>> or
>>> the deprecated version of Data Libraries no tab character is added. Do
>>> you
>>> have some idea to correct this problem? Thanks a lot Best regards --
>>> Fabien Mareuil | Centre d'Informatique pour la Biologie
>>> fabien.mareuil(a)pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux
>>> 75015
>>> Paris, France
>>>
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