I’m looking to use MetaPhlAn3 to profile some metatranscriptomics data I have. I have three files per sample:
sample1_R1.fastq.gz - forward reads passing QC with matching reverse read in R2 file
sample1_R2.fastq.gz - reverse reads passing QC with matching forward read in R1 file
sample1_unpaired.fastq.gz - reads that only one of the pair passed QC
I’m curious about the best way to go about running the profiling. Would the best way be to run MetaPhlAn with the three files following this command (found in help manual via metaphlan -h)?
metaphlan sample1_R1.fastq.gz,sample1_R2.fastq.gz,sample1_unpaired.fastq.gz --bowtie2out sample1.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_sample1.txt
Or is there an advantage (or disadvantage) to joining the paired reads before running MetaPhlAn? I read in the old Google Group that MetaPhlAn does not use the paired information in the reads and I am curious if joining the paired reads would be advantageous in analyzing the data. If I did join the reads (R1 and R2) would it be acceptable to run MetaPhlAn3 with the new joined reads and the unpaired reads?