I used a Tophat 2 analysis and got 99.2% discordant in the summary, while
in fact I checked the distance between the reads and got 170 with
std of 35 (this is the data i filled in the Tophat2).
Why did the Tophat2 test found 99.2% discordant when it should have been
The starting reads was 16665209, in a Bowtie2 test i got a logical outcome
of 16567482, while on the other hand i got from Tophat2 35066991 and
34816158 - not logical.
I tried to do the same test number of times with another data and got
resemblance in the results.
In all of the tests in Tophat2 i got discordant 99% and higher.
What am i doing wrong?
What is the correct way to feed data into the test?
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