Heatmaps of the metagenomes --> mapping file?

[WebBach]

Hi, Thanks for such useful tool! I've been following your Example 03: Metagenomic application - Metagenomic analysis of the Ethiopian cohort, but I got stuck in the least section of drawing heatmaps.

Step 3. Heatmaps of the top 21 SGBs found in the Ethiopian metagenomes

phylophlan_draw_metagenomic \
    -i output_metagenomic.tsv \
    -o output_heatmap \
    --map bin2meta.tsv \
    --top 20 \
    --verbose 2>&1 | tee logs/phylophlan_draw_metagenomic.log

where : is a mapping file that links each bin to the metagenome it has been reconstructed from. It is a tab-separated file where the input bins are in the first column and metagenomes in the second column

My issue is that I don't know how to obtain this --map file from my data. Which tool did you use?

Thanks :)

[fasnicar]

Hi, the bin2meta.tsv as described in the tutorial is a:

mapping file that links each bin to the metagenome it has been reconstructed from. It is a tab-separated file where the input bins are in the first column and metagenomes in the second column

The bin2meta.tsv file, as also reported in the tutorial:

For this example, we are providing the mapping file bin2meta.tsv present inside the example folder.

is available in the PhyloPhlAn repository here: https://github.com/biobakery/phylophlan/blob/master/phylophlan/examples/03_metagenomic/bin2meta.tsv

No tool was used to create that file, but it has been derived by simply considering which MAGs were metagenomically-assembled from what metagenome file.

I hope it is clearer now.

Thanks, Francesco