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



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http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
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