Hi Si,

Would you like to share your history with me? Note which dataset has the run with the issue and make sure that all inputs, including upload and Fastq Groomer (if done), are present and undeleted.


How to share:
https://wiki.galaxyproject.org/Support#Shared_and_Published_data

Thanks!

Jen
Galaxy team

On 4/6/14 6:54 AM, Si Naftaly wrote:
Hello,

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 much lower?

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?

Thank you

Si.




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