18 months ago by
Mapped reads are those that were aligned by the tool used (HISAT, Bowtie, etc) with respect to the other given inputs. Meaning, the fastq sequence "mapped" has homology to the target transcriptome/exome/genome that passes the threshold criteria set in the parameters.
Unmapped reads are those that were not aligned.
Galaxy wrapped tools are usually a way to work with an underlying 3rd party tool that is also available line-command. Links to these 3rd party tool manuals are usually given on the tool forms, but if you are using one without the link, you can also just google the tool name to find the manual and other online resources (google groups and other forums). Most tool forms have some documentation included that associates the line-command parameters with the web-based tool form's options. The tool wrapper code can also be examined if that is something you are familiar with reviewing or just want to try. However, should any be unclear let us know and we can offer help.
Filtering mapping results before calling variants is generally needed yet sometimes filtering after (or both) is the best practice workflow. Please see the Variant analysis tutorials and other NGS learning resources here for rational and examples: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team