Cannot use sbt.json file (sourmash search)

ctb commented 6 years ago

Hi eileen, did you figure it out?? :) let us know if we can help.

EileenNeelie commented 6 years ago

Hi Titus,yes I solved the problem. :-) Thank you! You really do some great work! Best, Eileen

ctb commented 5 years ago

On Fri, Sep 14, 2018 at 08:15:05PM +0000, EileenNeelie wrote:

Hi Titus,yes I solved the problem. :-) Thank you!You really do some great work!Best, Eileen

great, glad to hear it!

EileenNeelie commented 5 years ago

Hi Titus,

I have another problem and I am not really sure what I can do:

But I think I should give you a bit more background:

We did some Stabel-Isotope Probing (SIP) experiments and labeled bacteria capable of degrading a specific substrate. Then we did metagenomic sequencing and amplicon sequencing (16S rRNA) to identify what bacteria are involved in the degradation and to look into possible pathways. I assembled and binned the metagenomes, checked there quality and annotated then a few of the Metagenome assembled genomes. One of them seemed really interesting for our study, so I wanted to use sourmash to rapidly compare this MAG against some metagenomes, just to get an idea of if its present before doing mapping to get abundance. Now I choose 3 metagenomes and in additions the sig files from the Tara Oceans (Delmont), however, I did not get any hits at all.

To be on the safe side, I thought I also run it against closely related genomes (Desulfuromonas and Thermincola) since this should give me some "hits" and could be used as a "control". Now my problem: Even when using 'sourmash search' against the "control" genomes, I do not get any similarity matches between my MAG and those genomes and I think I should get some matches.

Do you have an idea what went wrong or what could be the problem?

To give you an idea what I did, I attached a file for you summarizing what I did.

I also attached the bin of interest for you (contigs and sig file) just in case there might be a problem with that?

Thank you!

Best wishes,

Eileen

Dr. Eileen Kröber Postdoctoral Researcher

Research Area 1 “Landscape Functioning“

WG "Microbial Biogeochemistry" Leibniz Centre for Agricultural Landscape Research (ZALF) Eberswalder Str. 84 15374 Müncheberg

Germany

Tel.: +49 / 33432 / 82-4085 Fax: +49 / 33432 / 82-343

e-mail: Eileen.Kroeber@zalf.de mailto:Eileen.Kroeber@zalf.de

Scientific Director: Prof. Dr. Frank Ewert Administrative Director: Cornelia Rosenberg Court at which the institute is registered as VR 35 35 FF: Amtsgericht Frankfurt/Oder VAT-ID: DE811417184

"C. Titus Brown" notifications@github.com hat am 14. September 2018 um 14:50 geschrieben:

Hi eileen, did you figure it out?? :) let us know if we can help.

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--> Make signature from 13C_Heavy1_Bin4 (MAG) sourmash compute --scaled 10000 -k 31 /Users/eileen/Desktop/sourmash/data/13C_Heavy_1_Bin4.fa -o /Users/eileen/Desktop/sourmash/sourmash/13C_Heavy1_Bin4.sig

--> Make signature from metagenomic reads (Marine metagenome 1) Sourmash compute --scaled 10000 /Users/eileen/Desktop/sourmash/data/Metagenomes/1/3300025895.a.fna.gz -o /Users/eileen/Desktop/sourmash/sourmash/marine_metagenome_1.sig -k 31

--> Evaluate containment, that is, what fraction of the read content (Marine metagenome 1) is contained in the ref genome (MAG - Bin4). sourmash search -k 31 /Users/eileen/Desktop/sourmash/sourmash/marine_metagenome_1.sig /Users/eileen/Desktop/sourmash/sourmash/13C_Heavy1_Bin4.sig --containment