tophat seq length qual length mismatch error

[epi]

I am getting a seq length-qual length mismatch with tophat (2.0.0 and 2.0.3). Has anyone seen this or knows possible remedy. Surprisingly same program with same input work fine on a different system. A different input works fine on the same system. Confusing as hell so far .... any comments plz

I see this error is posted before, but none of the explain my case. I have illumina 50 bp PE

[2012-07-07 02:23:20] Mapping test_reads against mm9 with Bowtie2 
[2012-07-07 08:51:26] Preparing reads
        [FAILED]
Error running 'prep_reads'
Error: qual length (50) differs from seq length (9) for fastq record !

[Richard Barker]

I'm having a similar issue, for one of my files TopHat 2 and Bowtie 2 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?

[Simon Anders]

Well, have you checked whether the quality and the sequence length are consistent in your FASTQ file? (Your post sounds a bit as if you used some tool for trimming but then did not inspect your FASTQ file by actually looking into the file.) Make sure to look at least at the beginning, the middle and the end of the file.

[TEFA]

Well, have you checked whether the quality and the sequence length are consistent in your FASTQ file? (Your post sounds a bit as if you used some tool for trimming but then did not inspect your FASTQ file by actually looking into the file.) Make sure to look at least at the beginning, the middle and the end of the file.

Hello,

I have the same error after to use cutadapt. In my case, I have discarded some reads that contains a defined sequence by using cutadapt and I have filtered out all the unmated reads...
Using Tophat I got the follow error, while the original files work well:

Error: qual length (18) differs from seq length (36) for fastq record !

The files at the beginning, the middle and the end look OK.... indeed, I have tried FASTQ groomer (Just to try, because my data are in sanger format) but the error changed.

Error: qual length (0) differs from seq length (36) for fastq record !

Have you solved your issue????

TEFA