Re: [galaxy-dev] automatic adding of a tab in a fastq header
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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