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Old 01-15-2013, 10:30 AM   #1
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
Default Tophat error: Error: qual length (113) differs from seq length (101) for fastq record

I am getting a couple of errors like this on two out of 18 of my files. Has anyone seen this and if so, does anyone know what it means or how to fix it?

JenBarb is offline   Reply With Quote
Old 10-20-2016, 09:07 AM   #2
Location: Virginia

Join Date: May 2016
Posts: 80

As suggested by GenoMax, try this command to examine the offending record by pulling it out of the file
$ cat (or zcat) <fastq_file_name> | grep <sequence_identifier> -A 3
ronaldrcutler is offline   Reply With Quote

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