Hello,

Great database, thank you!

1. I see in the summary image in the pipeline/tutorial section "KO Pathway" is listed for the functions section , although I don't see a way to arrange the KO annotations into pathways using the current tools - is that something that is still being worked on or am I missing the script for it somewhere here? Do I need to move my data into some KEGG specific pipeline to get pathway sums?

2. Is there an easy way to stratify KOs by taxonomy? I can get taxonomy TPM sums, and KO TPM sums, but it's not clear to me how to get KO sums by taxonomy. Thanks for any info you can provide!

Hello,

I am trying to use iMGMC for picrust analysis using the following code:

conda create -n iMGMC-PICRUSt -c bioconda picrust pynast fasttree
./iMGMC-PICRUSt.bash run2_feature.biom run2_sequences.fasta

As detailed in the picrust information page. But it seems I am missing a number of required files such as:
iMGMC-CopyNr-16SrRNA.tab
iMGMC-KO_traits.tab
along with a number of other traits files

I can't seem to find these files as part of the downloads on here - am I supposed to generate these somehow?

Thanks for your advice

Hello, I see how the .tab files connect genes and their associated function/taxonomy to the contigs they were annotated in, but is there coordinate information available that describes where in those contigs each ORF starts/stops? Thanks for info you have!

Hello, thank you for this great resource. If I'm not mistaken, you didn't submit your genomes to NCBI. I know it can be difficult sometimes. But the advantage of genomes submitted to NCBI is that they are incorporated in GTDB and other databases ..

If you provide me with a table with the NCBI sample names we can upload your genomes to NCBI and link it to your publication/Bioproject.

Kind regards

CC @ trickovicmatija

Hi Till

I get the error "usage: conda [-h] [-V] command ...
conda: error: unrecognized arguments: picrust pynast fasttree" when I key conda create iMGMC-PICRUSt -c bioconda picrust pynast fasttree
Do you know how to solve this issue?

Also I would like to use PICRUSt 2 with my amplicon sequences with your reference database. Do you have the PICRUST2 ready files in the following format?
pro_ref.fna.gz
pro_ref.hmm
pro_ref.model
pro_ref.tre

If not, I would greatly appreciate some guidance on how to get the files ready for PICRUST2.

thank you, kind regards
Adrian

Hi,
It's really an exciting tool for the mouse gut microbiome analysis! In my study, I have obtained the 16S rRNA gene V3-V4 amplicon sequencing data of C57BL/6J mice. I'm trying to use the pre-build links between 16S rRNA genes with metagenome-assembled genomes in iMGMC. In the paper, full-length, unique 16S rRNA gene sequences were used to build the links with metagenome-assembled genomes. I'm wondering if my 16S rRNA amplicon sequencing data could also employ this tool to get the metagenome-assembled genome informations? With this pipeline Instruction to process your own WGS samples with iMGMC? Many thanks!
Regards!

Does not produce the required directory for the next step.

This results in

Hi,
thanks to your great resource, I could match one differential abundant PacBio fulllength 16S feature to your mgs16S-0293. You assign the taxonomy Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Alistipes to it and I'd love to find our more about this specific bug.
Your Graphical Abstract says something about 168,573 SRA samples as input for your pipeline. Do you have some table lists prevalence of mgs16S-0293 in all those samples?
I am looking for something like our S6 table with more than the 11 broad categories.
Thanks in advance,
Stefan

Dear iMGMC developers,

Thanks for developing this amazing tool.
I was wondering if I could use iMGMC tool/data in order to assign 16S V4 ASV against a reduced, mice-specific microbiota database.
I obtained those ASV using the dada2 pipeline und ultimately would like to assign taxonomy using DECIPHER::IdTaxa().
So I would need a fasta file with mice specific 16S sequences as well as the taxonomic path.

Does it sound feasable? Would you suggest another alternative?

Thanks a lot for your help.

Flo

The file
"final-unambiguousReads.tab" does not get created. Also, there is no mention of it in the script from the screenshot below

from the linking tutorial.
Maybe that's an error in the documentation

I couldn't run bbmap if follow the command you mentioned in genecatalog-pipeline.md.
my BBmap version=38.86

bbmap.sh -Xmx30g unpigz=t threads=${usedCores} minid=0.90 \
ref=${iMGCM-data} nodisk \
statsfile=${SampleName}.statsfile \
scafstats=${SampleName}.scafstats \
covstats=${SampleName}.covstat \
rpkm=${SampleName}.rpkm \
sortscafs=f nzo=f \
in=${SampleName}_R1_rmhost.fastq.gz \
in2=${SampleName}_R2_rmhost.fastq.gz

I have to use "path" instead of "ref". Otherwise, BBmap fails to find the index.
Besides, I don't know whether it happened in your system, but minus symbol could not use in RedHat as an environment variable name.
Hope I can hear from you soon.