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Old 07-17-2012, 06:53 PM   #1
Location: asia

Join Date: Jul 2012
Posts: 38
Default qual length error when run tophat

Hi, All,
I am using tophat to process RNA-seq data from Illumunia genome analyzer IIx. I get the error when I treat one in a fastq data set while the other one in the same dataset is fine. I use the same parameter. I really don't undertant why! Could anyone help? Error is below(I have put --solex--qual parameter in my command line.) :

[2012-07-17 19:25:28] Beginning TopHat run (v2.0.4)
[2012-07-17 19:25:28] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version:
[2012-07-17 19:25:28] Checking for Samtools
Samtools version:
[2012-07-17 19:25:28] Checking for Bowtie index files
[2012-07-17 19:25:28] Checking for reference FASTA file
[2012-07-17 19:25:28] Generating SAM header for mm9
format: fastq
quality scale: solexa33 (reads generated with GA pipeline version < 1.3)
[2012-07-17 19:27:10] Reading known junctions from GTF file
[2012-07-17 19:27:22] Preparing reads
Error running 'prep_reads'
Error: qual length (0) differs from seq length (36) for fastq record SRR390298.!
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Old 08-12-2012, 02:54 PM   #2
Richard Barker
Location: Madison wisconsin

Join Date: Apr 2012
Posts: 47

I'm having a similar issue, one of my files worked fine then when i tried the next i got this error...
Error: qual length (121) differs from seq length (87) for fastq record !

The fastq files were unzipped and then had the first 15 bases trimmed off, could this have caused the quality score to differ from the sequence length?
Richard Barker is offline   Reply With Quote

qual length, rna-seq, tophat

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