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ohlab / GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
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Question on Pathoscope #10

Closed santoshe1 closed 5 years ago

santoshe1 commented 5 years ago

Hi Team,

I had a question regarding the GRiD Results. I used GRiD with and without Pathoscope option. I find that the number of genomes identified by using Pathoscope is really low in comparison to GRiD without Pathoscope for multiple samples. For ex, I get about 65 genomes only identified using Pathoscope where as I get about 1000+ genomes without it. Also, is GRiD with -P only considered only for ambiguous reads ?? Could I merge this results while using it without -P option??

Thank you

santoshe1 commented 5 years ago

I also observe that results are totally different on using Pathoscope and not?

aemiol commented 5 years ago

Hi, This is totally expected. If you have a read mapping to multiple genomes, Pathoscope identifies the most likely genome where the read comes from. Thus, you will have much less genomes using the -p option.

You can find out more about Pathoscope from https://sourceforge.net/p/pathoscope/wiki/Home/

Regards, Tunde

santoshe1 commented 5 years ago

Thank you for the quick response Dr. Tunde. Would it be then better to consider only the results from Pathoscope if you suspect to have more ambiguous reads?

aemiol commented 5 years ago

Yes. I will accept the results with Pathoscope since it is unlikely there will be over 1000 different species in a sample (as you saw without Pathoscope).

Cheers, Tunde

santoshe1 commented 5 years ago

Thank you again for your response Dr. Tunde. I have one more question, I have read your paper and it mentions you have observed Propionibacterium acne in one of the results. However, I am unable to find the same organism in the metadata of the database_misc.txt file. Could you please help me out and provide if you have any other detailed metadata file for the genomes/species_strain information?

aemiol commented 5 years ago

Propionibacterium acnes is now scientifically referred to as "Cutibacterium acnes". You should find that in database_misc.txt