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



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