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@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
replaced by a tab.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 <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
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