Paired-end reads analysis in Metaphlan2

Question

[yana.yatseviuk]

Hello to all! I would like to ask for some advice. I'm currently trying to analyze taxonomy of the metagenome from river floodplain, for what I downloaded SRA file from NCBI and converted it with fastq-dump and --split option to two fasta files (forward and reverse reads). Then I used Metaphlan2 for both fasta files separately. What I see in results - its % difference in taxonomic abundance between this 2 files. My question: should I merge this results in order to receive a full picture, or I shouldn't have split files with fastq-dump at the beginning? I will highly appreciate any help, as I'm a little bit confused how to proceed here.

Answer 1

[Sej Modha]

MetaPhlan2 does not support paired-end analysis so it would be better to run the analysis on each file and then merge the output to get the full picture of the data or if the paired-end information is not going to be used to run any further analysis such as assembly then it is better to avoid --split in fastq-dump command.

[yana.yatseviuk]

Thank you for the reply! Would you recommend some specific tool for merging output results and analyze it statistically? I'm thinking of using STAMP. Also, I tried to visualize through MEV, but stuck on the "Processing" message.

[luyang1005]

Hi, Now I am also at the same stage as you. Could you give me some suggestions on the paired-end shotgun data analysis? For using MetaPhlAn2, shall I need to merge the paired reads, and then use the MetaPhlAn2? Thanks in advance.