Thanks Jen for your answer
Zohra

> Date: Tue, 11 Oct 2011 13:01:37 -0400
> From: j...@bx.psu.edu
> To: saci...@live.fr
> CC: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] tophat error
> 
> Hi Zohra,
> 
> One more bit of help: in the past our team has noticed that Color Space 
> files from NCBI's SRA database have a "placeholder" adapter base quality 
> score added in (for an unknown reason).
> 
> If you choose to use Galaxy, when passing the file through the FASTQ 
> Groomer tool (with input and output type set to cssanger) this extra 
> score is removed. This standardizes the data and makes it useable with 
> analysis tools such as Bowtie/TopHat.
> 
> The same thing could be done on the command line (removing the initial 
> qual score for each FASTQ entry) if that is an option for you.
> 
> Best wishes for your project,
> 
> Jen
> Galaxy team
> 
> 
> 
> 
> On 10/11/11 12:14 PM, Jennifer Jackson wrote:
> > Hello Zohra,
> >
> > For command line (not Galaxy) use of this tool, questions would be best
> > directed to the tool authors at tophat.cuffli...@gmail.com. That said,
> > there appears to be a mismatch between the quality scores in your fastq
> > file and what was expected (integer, linked to the -C option).
> >
> > Should you decide to use Galaxy at http://usegalaxy.org, there are tools
> > to format the input and run this type of job. To help you get started,
> > please see our tutorial covering this exact type of analysis:
> >
> > http://wiki.g2.bx.psu.edu/Learn/Screencasts
> > see "Examples of other analyses -> SOLiD Single End"
> >
> > Hopefully one of these options will work out for you,
> >
> > Best,
> >
> > Jen
> > Galaxy team
> >
> > On 10/11/11 7:47 AM, zohra saci wrote:
> >>
> >>
> >> Hello,
> >> I was trying to run tophat v1.3.2 on SOLID data and I have this error:
> >> *zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4
> >> -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq
> >>
> >> [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
> >> -----------------------------------------------
> >> [Tue Oct 11 13:23:53 2011] Preparing output location
> >> /tmp/tophat_SRR036752//
> >> [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files
> >> [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file
> >> [Tue Oct 11 13:23:53 2011] Checking for Bowtie
> >> Bowtie version: 0.12.7.0
> >> [Tue Oct 11 13:23:53 2011] Checking for Samtools
> >> Samtools Version: 0.1.18
> >> [Tue Oct 11 13:23:53 2011] Generating SAM header for
> >> /home/zohra/indexes_bowtie/humain_
> >> [Tue Oct 11 13:23:55 2011] Preparing reads
> >> format: fastq
> >> quality scale: phred33 (default)
> >> [FAILED]
> >> Error running 'prep_reads'
> >> Error: qual length (51) differs from seq length (51) for fastq record !
> >> *
> >> Can you help me.
> >> Thanks
> >> Zohra Saci
> >>
> >>
> >>
> >> ___________________________________________________________
> >> The Galaxy User list should be used for the discussion of
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> >>
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> >>
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> >>
> >> http://lists.bx.psu.edu/
> >
> 
> -- 
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/Support
                                          
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