Hello Zohra, For command line (not Galaxy) use of this tool, questions would be best directed to the tool authors at tophat.cufflinks@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 Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support