Hi~, i am really new to use Strainphlan and Metaphlan. I have several general questions to help me really understand the whole pipelline.
- i have run MetaPhlan successfully with the codes as:
metaphlan path/to/reads/s1.forward.fastq.gz,path/to/reads/s1.reverse_reads.fastq.gz -o s1.tsv --input_type fastq --bowtie2out s1.bowtie2.bz2 -s s1.sam.bz2
but when i read others’ posts, i noticed that some are using different databases from chocophlan database with --bowtie2db; here I did not specify the database, will MetaPhlan uses default db?
2) After i get the species info from metaphlan, i want to use Strainphlan and get strain info. I followed the StrainPhlAn3 · biobakery/biobakery Wiki · GitHub
in step 3: ```
extract_markers.py -c s__Eubacterium_rectale -o clade_markers
I am wondering whether the -c s__Eubacterium_rectale means that we can only get the strain info for this only one s__Eubacterium_rectale species?? If so, how can I get all the possible strains info from all species in my file of metaphlan output? 3) in the same step 3, ``` strainphlan -s consensus_markers/*.pkl -m clade_markers/s__Eubacterium_rectale.fna -r reference_genomes/*.fna -o output -n 8 -c s__Eubacterium_rectale --phylophlan_mode fast --nproc 4
it also specifies the
-c s__Eubacterium_rectale and it needs the
-r reference_genomes/*.fna; do i need to curate the my own reference-genomes? or can i use the cholophlan database ?
Thank you so much