Convert reads alginment results of NGS metagenomic sample into abundance score
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6.1 years ago
benarnon ▴ 30

I have results of reads aligner of metagenomic  NGS sample versus small database of genes (I aligned the sample reads versus the small DB) . I want to convert the read aligner results into abundance score for each one of the genes in the database.

I saw that in a few articles they decided that the number of reads that were align for this gene is the abundance score but it sound to simple. Anybody has another idea of how to calculate this measurement?

Thanks

Metagenomic alignment NGS • 1.4k views
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6.1 years ago
glihm ▴ 630

Hi, 

I think that the abundance for each read can be a part of the score counting the number of reads. Then, the alignment quality can be considered, and with this designed an adjusted score. Because align read is good, but the quality of this alignment must be taken in account. 

I work with metagenomics from gene of 16S, and I am doing it. Counting the reads, and see the alignment score to normalize and ponder ate data.

But we need to find the description in articles that you mentioned, or contact them to understand how they are doing. ;)

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6.1 years ago
Len Trigg ★ 1.5k

One thing you could try is the species abundance tools included in RTG Core. While this has been designed for processing the alignments of metagenomic NGS data to a species reference database, people have been using it successfully for gene expression datasets. One of the advantages over read-counting approaches is that it takes ambiguity into account (alignments to ambiguous regions are less informative than alignments to unambiguous regions), and it also supports a taxonomy, so you could potentially obtain abundance measures for gene families. The abundance scores computed by the species command are represented both as a fraction of the DNA in the sample and as a fraction of individuals (genes). Hope this helps.

 

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