Question: Tophat2 : What is the difference between no-mixed and no-discordant?
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gravatar for irritable_phd_syndrom
2.2 years ago by
irritable_phd_syndrom60 wrote:

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.

rna-seq assembly • 898 views
ADD COMMENTlink modified 2.2 years ago by Devon Ryan88k • written 2.2 years ago by irritable_phd_syndrom60
1
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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).

ADD COMMENTlink written 2.2 years ago by Devon Ryan88k
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