3.2 years ago by
This is correct - that option just subsets unaligned reads so that they can be easily worked with again (for example, to check for contamination/artifact).
Any BAM/SAM dataset can be filtered to remove unmapped reads. Use tools from the tool group "NGS: SAM Tools". Convert to SAM when needed, then filter. You can create a mini-workflow to do this automatically, along with the Tophat2 run, and hide the intermediate datasets (and then go back later to permanently delete them if you start to run out of space).
If you are interested, there are a few other Tophat2 options that may suit your case. These are not yet implemented in the Galaxy wrapper, but are listed in the manual, should you ever be running the tool line-command.
||For paired reads, report only concordant mappings.
For paired reads, only report read alignments if both reads in a pair can be mapped (by default, if TopHat cannot find a concordant or discordant alignment for both reads in a pair, it will find and report alignments for each read separately; this option disables that behavior).
Hopefully the post-Tophat filtering will work out for you, it is what most people choose to do. Jen, Galaxy team