Hi @TTP
Most tools in Galaxy expect reads in fastqsanger or fastqsanger.gz format and with one of those datatypes assigned. Those datatypes represent a specific type of quality score scaling: Sanger Phred +33.
This is produced by Illumina 1.8+ pipelines. PacBio used Phred+33 scaling to start with and now the scaling is neutral. You can double check with a tool like FastQC or FASTQ info to see what those report.
There are some tools that expect just fastq or fastq.gz (scaling unspecified). But if you are ever not sure what datatype(s) a tool accepts as input, any tool not just those that accept reads, try this:
- Create a new empty history
- Load up the tool form
- Review the input datatypes listed in the tool form’s input area
- Note: A tool could have more than one input area and this works for all user-supplied inputs from the history.
Example
