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.
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.