1
$\begingroup$

I have a metagenomic dataset across multiple samples that has been grouped and binned (we did this due to poor sequence quallity).

It is several samples taken from termite guts of differing castes, the samples have been grouped to make binning easier due to poor sequence suitability. They have been binned via ASVs, assembling reads from all samples to generate the putative bacterial species. So I have fasta files of putative species that have been annotated via prodigal. I want to now calculate the abundance of each bin in a given sample. I think the best way to do this would be at the gene level by looking at the number of reads that map to a gene in any given sample. I am just unsure how to do this.

I have annotated the bins and now want to calculate the abundance of each bin in a sample but looking at the number of reads from a sample that map to each gene in a bin.

Is this a viable method? If so how would I do it and if not what else could I do?

$\endgroup$
0
1
$\begingroup$

The best way to approach it would be to take trimmed reads map them to the bins (i.e. with bowtie2) and estimate the abundance of each bin with samtools by getting the depth of coverage:

https://www.metagenomics.wiki/tools/samtools/breadth-of-coverage

or you can use QUANT_BIN module from the METAWRAP to do it for you. Follow this for the METAWRAP approach:

https://github.com/bxlab/metaWRAP/issues/40

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.