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map full 16S rRNA genes and extract OTU table #5

Open lucaz88 opened 3 years ago

lucaz88 commented 3 years ago

Hi, I have a set of full length 16S rRNA genes (~500) that I want to map against other studies with the goal of determining the occurrence (maybe even relative abundance) of my 16S in other microbiomes. From what I have read in the 'About' section of the microbeatlas.org and from issues #1, this task should be possible by using MAPseq however, at the moment most of the links (all?) on the result page throws an java script error and I cannot see how to download the matching OTU tables. Is there a way to download the Microbe Atlas db and run the analysis on my laptop?

Thanks for your help, Cheers Luca

grexor commented 3 years ago

Dear Luca,

Thank you for your interest in microbeAtlas. We use a reference of taxa in microbeAtlas (1M taxa). One way to get abundances across samples would be to find (identify) the 500 taxa, either by name or using MAPseq. For example, you could paste one 16S gene in the MAPseq window and identify which microbe aligns best. Then, when opening the link to the microbe (=taxon=OTU), you can download sample abundances across all samples where the microbe was detected (Download, top right in the abundance table).

Hope this helps,

Cheers, Gregor

lucaz88 commented 3 years ago

Dear Gregor,

thanks a lot for your answer!

I paste and submit my ~500 sequences at once using MAPseq. Then from the abundance table, I can download (top right) the list with all the hits e.g. "B16S;90_392;96_884;97_1024    5    gene_2561511239    gene_2503283017    gene_2503982040    gene_2751185908    gene_GCA_000012345". However, now I have to manually click on each hit and download the abundance table from the related web page. Is there a way in which I can do this last step "in batch"? As I'd like to avoid having to manually click and download the abundance table for all the hits.

Cheers

Luca

-----Original message----- From: Gregor Rot notifications@github.com Sent: Saturday 6th February 2021 16:45 To: meringlab/MicrobeAtlasWebsite MicrobeAtlasWebsite@noreply.github.com Cc: Luca Zoccarato zoccarato@igb-berlin.de; Author author@noreply.github.com Subject: Re: [meringlab/MicrobeAtlasWebsite] map full 16S rRNA genes and extract OTU table (#5)

Dear Luca,

Thank you for your interest in microbeAtlas. We use a reference of taxa in microbeAtlas (1M taxa). One way to get abundances across samples would be to find (identify) the 500 taxa, either by name or using MAPseq. For example, you could paste one 16S gene in the MAPseq window and identify which microbe aligns best. Then, when opening the link to the microbe (=taxon=OTU), you can download sample abundances across all samples where the microbe was detected (Download, top right in the abundance table).

Hope this helps,

Cheers, Gregor

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csanchis commented 1 year ago

Hi, I have a similar question, but I would like to search at once more than 10,000 of 16s sequences, so is it available the reference taxa in microbeAtlas somehow, for performing a local MAPseq search? Thank you very much