How Tophat2 deals with unpaired matches?

[julio514]

Hi all,
I'd need some help with this. I noticed that Tophat2 will disrupt paired end reads if say for a given pair of reads fwd read matches but rev read does not. Is there an option to prevent that? I d'like Tophat to only report mapped paired reads (fwd read AND rev read).

On the Tophat manual I saw the option --no-discordant. But seems to be deprecated in Tophat2.

Any help would be appreciated - thanks!
Julio

[kmcarr]

Hi all,
I'd need some help with this. I noticed that Tophat2 will disrupt paired end reads if say for a given pair of reads fwd read matches but rev read does not. Is there an option to prevent that? I d'like Tophat to only report mapped paired reads (fwd read AND rev read).

On the Tophat manual I saw the option --no-discordant. But seems to be deprecated in Tophat2.

Any help would be appreciated - thanks!
Julio

Julio,

I think you have that backwards. The '--no-discordant' option was just added in in the very latest version of TopHat2 (2.0.4). The default behavior in 2.0.4 is to report discordant alignments, you turn off this default with '--no-discordant'.

In earlier versions of TopHat2 (at least 2.0.0 and 2.0.3 which are the ones I was able to check) the default behavior was to NOT report discordant alignments. You could override this default with '--report-discordant-pair-alignments'. It is this option which has been deprecated.

You should also check the documentation for the '--no-mixed' option in 2.0.4

[julio514]

Ok I see. I'll give it a try. Thanks Kmcarr!
J