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 When I look the file in a history, the space between @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been replaced by a tab.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&gt; > 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&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/ >>