Tophat Error

Question: Tophat Error

7.1 years ago by

zohra saci • 20 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

alignment bowtie samtools bam • 1.9k views

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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by zohra saci • 20

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD REPLY • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen for your answer Zohra

ADD REPLY • link written 7.1 years ago by zohra saci • 20

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