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 <fmare...@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 <fmare...@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.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux
>>> 75015
>>> Paris, France
>>>
>>> ___________________________________________________________
>>> 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:
>>>    https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>    http://galaxyproject.org/search/mailinglists/
>
>
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to