Hello,

I wanted to use UGENE for taxonomy classification of NGS paired end reads. I modified Kraken - Clark workflow (by removing Clark part) so only improving reads with Trimmomatic and Kraken classification left. My problem is that when I use this combination I get only output for a second pair of processed files, while when I remove Trimmomatic part Kraken gives me multiple outputs for each pair proceseed. What can i do to use Trimmomatic and Kraken combination and to obtain taxonomy classification for each analysed file at the end? I would really appreciate your help. I checked forum but I did not find my problem to be discussed there.

Cheers,
Marta

Hello, Marta,

I'm sorry for the delayed answer.

It's difficult to find a problem because I have a very vague view of your actions. The best way for you to give me chance to figure the problem out is to save the resulting workflow (the "Save workflow as" button on the toolbar) and send it to me with the data you use.

Also, I can make several suggestions:
1. Trimmomatic refuses the first pair, so Kraken doesn't have it as input. What steps did you set in Trimmomatic?
2. Click on the "Kraken" element, find the "Input data" box on the right and check, that the first slot has the first output by Trimmomatic and the second slot has the second output.

Bes regards,
Dmitrii Sukhomlinov,
UGENE team.