Comments (12)
I am very sorry for the inconvenience caused to you. If you have any questions in the future, I will do as you said.
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I am very sorry for the inconvenience caused to you. If I have any questions in the future, I will do as you said.I'm sorry for the typo in my last answer. I hope it won't cause your misunderstanding.
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Hi,
as written at https://github.com/BIONF/fDOG/wiki/FAQ#can-fdog-work-with-non-ncbi-taxa, the core compilation step of fDOG cannot work with non-ncbi taxa. I suppose that you have your new species with the ID 39525383 in the blast databases folder (named coreTaxa_dir
by default).
Best,
Vinh
P.S.: I see that you open multiple issues to ask about the problems regarding only to the usage of fDOG, i.e. they have always the same topic. It would be more convenient for us if you just post them in one ONE issue entry. Many thanks!
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Hi,
There was a strick option in an earlier version of Hamstr. I wonder if there is an option in fDOG that has similar functionality to strick.Or in other words how to make the software run more accurately.
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The -strict
option is not available anymore in fDOG. I would suggest to choose from the core taxa the reference species as the most closely related species to your search taxa.
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Ok, thank you very much for your reply
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Sorry to bother you again, but the choice for the --evalHmmer parameter should be 0.00005 or 1e-6
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you must use the decimal format (e.g. 0.00005 for 5e-5)
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Hi,
There was a strick option in an earlier version of Hamstr. I wonder if there is an option in fDOG that has similar functionality to strick.Or in other words how to make the software run more accurately.
Hi @majssssa ,
just another info, we found that fDOG performed with a high specificity. The -strict option will just reduce the sensitivity, which is not necessary. You will find this benchmark in the fDOG manuscript, which will be soon published.
Regards,
Vinh
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HI,
When running fDOG, I added the --rbh option instead of the --rsp option. I found that only one gene was selected for each species. Is this because the conditions are more stringent after adding --rbh, so only one gene meets the criteria, or does the --rbh option select only the most perfect candidate based on the output?
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Related Issues (20)
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- extend taxonomy ranks for core compilation
- fdog cannot identify correct input seed sequence HOT 1
- about the seed sequence HOT 2
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- Avoid editing `~/.bashrc` without user permission HOT 6
- Convert six assignment statements to augmented source code HOT 2
- FileNotFoundError: [Errno 2] No such file or directory: '~/python3.7/lib/python3.7/site-packages/fdog/bin/pathconfig.txt' HOT 3
- 4180 low-copy lineologous candidate nuclear genes from 9 representative angiosperms HOT 8
- http://www.deep-phylogeny.org/hamstr HOT 1
- ERROR: Cannot find seed sequence in genome of reference species for Dracaena_cambodiana_DN10000_c0_g1_i1.p1! HOT 4
- select Candidate Orthologous Genes (OGs) from transcript of transcriptomes HOT 9
- Isoforms
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- Addition of Taxa doesnt seems to be working with fdog.addTaxa HOT 8
- question for understanding the input files for HaMStR, --seqFile and --refspec
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- rename seq IDs back to original IDs
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