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hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
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Detection of Eukaryotic genes seems not to work #70

Closed taltman closed 7 years ago

taltman commented 9 years ago

Using Kraken, I identified several contigs in my sample that were of eukaryotic origin. Yet in the protein taxonomic annotation, no eukaryotic genes were identified. I suspect that prodigal is only being run with the common bacterial translation table, and thus it might be missing eukaryotic genes. Is this the case?

gwilymh commented 8 years ago

I found the same problem, taltman. I ran Metapathways 2 using the RefSeq protein database. The only Eukaryotic taxonomic classifications were: cellular organisms (131567), Euryarchaeota (28890), Marine Group II euryarchaeote SCGC AB-629-J06 (1131268) and unclassified Euryarchaeota (33867)

I am working with seastars, so I am able to partially get around this by downloading the sea star genomes from echinobase and adding them to the rRNA databases. Any hits to one of these genomes indicates that I likely have a sea start DNA sequence and not some contaminating marine microorganisms.

(The database was downloaded from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete/complete.nonredundant_protein.N.protein.faa.gz, where N=1…309; and files were unzipped and concatenated into a single master file used by Metapathways)

hallamlab commented 7 years ago

yes, right now MP supports only prokaryotic data

taltman commented 7 years ago

Has this been implemented?

ariahahn commented 7 years ago

No, this requires several new modules (like alternative orf prediction) and some tools that currently do not exist (such as a method by which to split euks and prots at the nucleotide level reliablly). MP is a eukaryotic pipeline as it stands. Perhaps a phase 2 project?

On Jan 10, 2017 3:53 PM, "Tomer Altman" notifications@github.com wrote:

Has this been implemented?

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