[galaxy-user] tophat error

[Jennifer Jackson]

Hello Zohra,

For command line (not Galaxy) use of this tool, questions would be best 
directed to the tool authors at tophat.cufflinks at 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 at 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
>
>
>
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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support