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&gt; > 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 >> >> ___________________________________________________________ >> 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/