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.
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written
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irritable_phd_syndrome •
1 answer
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).
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