summarise metagenomics results

[LeonardosMageiros]

Hi,

I have recently executed card bwt for a set of metagenomic reads that I have and I would like to summarize my results in one table so I can compare my samples.

I was wondering if you have such a script available before I dedicate time to write it myself.

Additionally could you briefly explain the difference between the result tables at the allele and at the gene level as I am not sure I get it?

Thank you in advance for your time. Best Leonardos

[raphenya]

I was wondering if you have such a script available before I dedicate time to write it myself.

We don't have a script to summarize results added to rgi repository yet. But you are welcome to see work done located here comparing sewage samples.

Additionally could you briefly explain the difference between the result tables at the allele and at the gene level as I am not sure I get it?

The allele tab-delimited contains results of aligning reads to reference sequences e.g

allele level

cat ERR1725954_wild.allele_mapping_data.txt | cut -f1,2,3 | grep "OXA-2|"
ARO:3001397|ID:1118|Name:OXA-2|NCBI:M95287.4	OXA-2	3001397
Prevalence_Sequence_ID:146105|ID:1118|Name:OXA-2|ARO:3001397	OXA-2	3001397
Prevalence_Sequence_ID:151926|ID:1118|Name:OXA-2|ARO:3001397	OXA-2	3001397

gene level

cat ERR1725954_wild.gene_mapping_data.txt | cut -f1,2,3,4 | grep "OXA-2"
OXA-211	3001710	protein homolog model	CARD; Resistomes & Variants
OXA-2	3001397	protein homolog model	CARD; Resistomes & Variants
OXA-210	3001487	protein homolog model	CARD
OXA-23	3001418	protein homolog model	Resistomes & Variants

we consider each row from allele tab-delimited as alleles for AMR determinant / gene OXA-2. We then summaries by gene in the gene tab-delimited. Hope that makes sense.

[miguensblanco]

Hi guys,

Thanks first for the great tool and the rest for the interesting threads in the repository.

However, I am trying to assemble a table as it was originally suggested in this thread. I have to reckon that (sadly) my python skills did not go (yet) beyond follow instructions to run scripts,etc.

I had tried to run create_heatmap_data.py from the repository that Amos provided in the previous post with no luck (short line to get to the desperate state where I am now :sweat_smile: )

I am asking if anyone has come with a basic table that summarize results so I could compare the samples in the downstream analysis?

I will really appreciate any help or link that could help the cause :)

Cheers,

Jesus

[raphenya]

Closing this issue. Please @LeonardosMageiros and @miguensblanco, re-open if you still need help on this. Cheers.