User: agata88
agata88 • 610
- Reputation:
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- Poland
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- http://bioidea.com.pl/en
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- 20 hours ago
- Joined:
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Posts by agata88
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... Hi all!
I was testing assign_taxonomy.py and summarized_taxa.py scripts for my own reference from NCBI.
My reference was created as GreenGenes reference (fasta and taxonomy file), except that mine contains only species taxonomy (full 16S gene). Since I've made it compatible with qiime I observed ...
written 1 day ago by
agata88 • 610
• updated
1 day ago by
kennethcondon2007 • 840
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Comment:
C: Good quality mock community?
... Thanks, but I am not sure if there are fastq files? for example for HM-782D mock community. I am looking for fastq R1/R2 reference which will include exactly 20 species - not stored fastq file of published data (which is very often deficient) ...
written 9 days ago by
agata88 • 610
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... Hi all!
Do you know any source of good quality fastq reads (MiSeq, HiSeq) of Mock Community with expected taxonomy?
I was working with mokrobiota but the fastq reads have very low quality and it is not possible to compare results.
Any help will be much appreciated,
Best,
Agata ...
written 9 days ago by
agata88 • 610
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C: Bioidea - open on taking on jobs
... A new post came out on Biodea Facebook page - Cell reprogramming as a breakthrough in healing wounds! - check out here: https://web.facebook.com/bioidea.bioinformatics/
Best,
Agata
...
written 9 weeks ago by
agata88 • 610
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... Hi!
I found post in biostar that might be helpful. https://www.biostars.org/p/216441/
To be curious, why do you have hetero variants if your organism is haploid?
Best,
Agata ...
written 10 weeks ago by
agata88 • 610
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... Hi all!
Feel welcome to visit our Facebook page of Bioidea - https://web.facebook.com/bioidea.bioinformatics/
This page is going to be used to inform you about the developments and the most interesting achievements connected with the world of genetics, microbiology and related sciences, with Next- ...
written 11 weeks ago by
agata88 • 610
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... Thank you very much for instruction to find this information :). I was searching PATRIC database before but I could not find it, so thanks!, Best, Agata ...
written 12 weeks ago by
agata88 • 610
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... I was thinking more about a database with pathogen bacteria species (e.g.. from NCBI) and related disease confirmed in publications. Do you know a database like that? I heard about PATRIC database but I cannot find those information there. ...
written 12 weeks ago by
agata88 • 610
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... Hi all!
Do you know a database where I can find bacteria pathogens with correlated disease?
Many thanks for help,
Best,
Agata ...
written 12 weeks ago by
agata88 • 610
• updated
12 weeks ago by
a.zielezinski ♦ 7.4k
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Comment:
C: Metagenome 16S reference
... hmm, yes indeed. I was using Silva124 version not the one you have used. I am gonna go with 128 version. Thanks. ...
written 3 months ago by
agata88 • 610
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For normalization of NGS results
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For A: Idenity, e value or bitscore ?
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