Hi @franzosa !!! As much as I know, for MetaPhlAn 3.0 we can catenate the forward and reverse reads into a single file. We can run that single file with
metaphlan command. Like that, can we also run this single file with kneaddata? I mean, should I run the forward and the reverse reads separately or I can run after concatenating them into a single file?
I think I have similar question… In general my question is that which Kneaddata output files should be used for Humann/Metaphlan? My input arer paired-end raw files (R1 and R2 fastq.gz). I am not quite understand the output files. For instance, in the tutorial (https://github.com/biobakery/biobakery/wiki/kneaddata) seq1 and seq2 should be R1 and R2 in my case, however only seq1/R1 came out after the running? What are the difference between *_1.fastq and *_2.fastq? Thank you.
Hi @Min-Ting , what is the command you are using?
Hi @DEEPCHANDA7, I used:
kneaddata --input SAMPLE_R1.fastq.gz --input SAMPLE_R2.fastq.gz --reference-db PATH/TO/REF/DATABASE --output SAMPLE_knead
Basically follow the manual directing for paired-end data.
HI @Min-Ting, If you use
--cat-final-output option, then the forward and the reverse reads are catenated to form a single file named like
*_1_kneaddata.fastq. You can feed this .fastq file for subsequent MetaPhlAn and HUMAnN analysis.