Question: Tophat prep_read error
gravatar for Yuka Takemon
4.4 years ago by
Yuka Takemon40
Yuka Takemon40 wrote:


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:
[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
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!

rna-seq tophat illumina • 1.8k views
ADD COMMENTlink modified 10 months ago by RamRS27k • written 4.4 years ago by Yuka Takemon40

Cheers Brian,

I think you're right. I ran into a common bug on Chrome, where users downloading large files will often have incomplete files. I am re-downloading all the data again using a different browser.


ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by Yuka Takemon40
gravatar for Brian Bushnell
4.4 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

If the error message is correct, your fastq file is corrupt; you should redownload it.

ADD COMMENTlink written 4.4 years ago by Brian Bushnell17k
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