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what's meaning of parameter "-t rel_ab_w_read_stats"

Hi all,

I am using metaphlan 3 to profile the microbial composition, and I found the difference between two parameters, specifically, the following parameters:

-t ANALYSIS TYPE      Type of analysis to perform: 
                     * rel_ab: profiling a metagenomes in terms of relative abundances
                     * rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads coming from each clade.
                     * reads_map: mapping from reads to clades (only reads hitting a marker)
                     * clade_profiles: normalized marker counts for clades with at least a non-null marker
                     * marker_ab_table: normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)
                     * marker_counts: non-normalized marker counts [use with extreme caution]
                     * marker_pres_table: list of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th
                    [default 'rel_ab']

the default is rel_ab, when using this parameter, the item relative abundances is proportion in output, the abundance in each level can sum to 100. However, when using -t rel_ab_w_read_stats, the abundance in each level cannot sum to 100, so what's meaning of relative abundance in this case? Can I directly compare their abundance between different groups? Thanks in advance!

metaphlan 3
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written by zhangdengwei zhangdengwei

Did you figure it out? I am also stuck at this step. Can you please help me out?

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written by dpc dpc

The output from rel_ab_w_read_stats should be reads count. You can convert it into proportion manually, which is akin to the output of rel_ab.

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written by zhangdengwei zhangdengwei

But when you convert it to relative abundance using -t rel_ab_w_read_stats , it is not same as of the abundance output from rel_ab

Thanks

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written by dpc dpc

But when you convert it to relative abundance using -t rel_ab_w_read_stats , it is not same as of the abundance output from rel_ab

Thanks

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written by dpc dpc

Could it be, that -t rel_ab_w_read_stats havn't been normalized to clade-marker coverage? But that would be in contrast to the name relative abundances with read stats.

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written by mario_de_manner • mario_de_manner

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