How to have the abundance of my bacterium of interest in a metagenomic dataset
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5.9 years ago
vin.darb ▴ 300

Hello everyone,

To explain, I have a SAG (single amplified genome) from a bacterium of interest, I have assembly reads into contigs (with SPAdes) and then I have extract the 16s RNA sequence.

I have also several metagenomics datas (filtered reads, ~100pb, ~200 000 000 reads) from differents lakes and the objectif is to calculate the relative abundance of my bacterium in these metagenomics datas.

For that, I thought about aligning the 16s RNA against the metagenomics reads with this simplified script:

for meta in metagenome: do blastn -evalue 1e-7 -db metadb -query ARN_16s -perc_identity 97 -outfmt 6 -out resultats/$meta/resultats.blasttab (I keep the hits only if the alignment is greater than 40pb)

The problem is that I have only few hits in the first lake, but no hits in the four others .. (I'm supposed to have results in the other lakes)

Did you thinks the parameters that I utilise are good ? (40pb for the alignement, evalue or perc_identity .. ?) Is my method good ?

Thank's in advance

gene genome next-gen • 1.2k views
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I recommend to add the code formatting around your code snippets for more clarity

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the 200M reads are from one or multiple experiments, whole genome shotgun or 16S amplicon seq?

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5.9 years ago
Tm ★ 1.1k

One of the fastest way of checking out the taxonomy of the metagenome data is using KAIJU webserver. You just have to upload the zipped metegenome reads file and can select the database of your choice.

After the process is completed, you have to download the result file where you can get information about the microbes identified along with its abundance.

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