Hello,

I am running a Tophat script that has worked previously, however with the new data set I am trying to map the sequence length and my quality length in all of my fastq files are incongruent (I am guess that quality length and sequence length are usually the same).

I am getting the following error message:

[2015-12-18 22:09:55] Checking for Bowtie
                  Bowtie version:        2.2.3.0
[2015-12-18 22:09:55] Checking for Bowtie index files (genome)..
[2015-12-18 22:09:55] Checking for reference FASTA file
[2015-12-18 22:09:55] Generating SAM header for /pathto/genome_index/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
[2015-12-18 22:10:04] Preparing reads
        [FAILED]
Error running 'prep_reads'
Error: qual length (47) differs from seq length (100) for fastq record !

Each fastq file has 100 seq length but varying qual lengths.

When running Fastqc, my reads seem normal with good quality score with no indication of different quality and seq lengths.

Am I understanding this error correctly and how do I fix this?

Thanks in advance!