4.4 years ago by
The format needs to be in ".fastqsanger". This wiki can explain how to determine what type of fastq data you have, if any quality score rescaling is needed, and how to reassign the datatype as needed.
Review this section and especially the following about FASTQ specifically. Correct datatype labels are important, but the underlying data must be a match in content for your analysis to come out with the correct answers:
BTW - this may have been a typo - but ".fastaq" is not a Galaxy datatype - I suspect that you meant to type ".fastq". If you happen to have ".fasta", you can still use Tophat2 with default quality scores. Use the tool "Combine FASTA and QUAL" to do this. Use default options and only provide the ".fasta" file as input.
Take care, Jen, Galaxy team