Tophat2 : What is the difference between no-mixed and no-discordant?

Question

[irritable_phd_syndrome]

What is the difference between the tophat2 options --no-mixed and --no-discordant? From the manual it says :

--no-discordant

For paired reads, report only concordant mappings.

--no-mixed

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)

Sounds like pretty much the same thing to me.

Answer 1

[Devon Ryan]

Discordant alignments can have the wrong relative orientation (in practice, these end up being "mixed") or internal distance. "mixed" alignments can include "singleton" reads (i.e., reads that had a mate that was ignored during the alignment).