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Old 08-05-2014, 05:10 AM   #1
khoojj
Junior Member
 
Location: Malaysia

Join Date: Aug 2014
Posts: 2
Question Questions: Reads scores for RDP Classifier files imported into MEGAN

Hi ALL! I'm new to this forum, and also new to the world of metagenomics data analysing. I would appreciate if anyone can enlighten me on this question.

Let me start my describing what I've done: I have some 16s sequences (from Ion PGM) which I have classified on RDPipeline Classifier using confidence threshold of 50 (for sequence shorter than 250bp). The classification.txt which I downloaded looked fine, with the taxonomic assignments and also the scores.

I then imported the classification.txt into MEGAN5, according to the instructions in the manual. I chose RDPstandalone as the format since the other option for RDP didn't work at all. I also included the fasta reads file. For the LCA parameters, I used all default values (min score=50).

After processing, MEGAN gave me a tree. However, when I chose the option to Inspect a node, I found that all my reads have a score of 100 even though the scores for some ranks in the classification.txt were less that 1.0. My questions: Is this normal? For all reads to have score of 100?

Below is an attachment of the screenshot of the Inspector window, showing 2 reads that have 100 scores, and the entries (ranks and scores) from the classification.txt

I thank anyone who takes the time to read this and help me out. Please let me know if im thinking along the right line and if any more clarifications needed.
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