User: kristjan

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kristjan110
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Estonia
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Environmental microbiologist

Posts by kristjan

<prev • 6 results • page 1 of 1 • next >
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Difference between plasmids from complete genomes and Refseq plasmids sequences
... Do you know how big is the overlap between the plasmids in ftp://ftp.ncbi.nih.gov/refseq/release/plasmid/ and the plasmids that come together with the individual genome assemblies from RefSeq? ...
refseq plasmids complete genomes written 17 months ago by kristjan110 • updated 16 months ago by Biostar ♦♦ 20
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Demultiplex paired-end reads with dual primers and barcodes
... We prepared an Illumina MiSeq library with double primers - one for bacteria and one for archaea and used the same barcodes with both primers. Now I have the sequenced paired-end reads that I want to split into groups, but every program that I have found is only using the barcodes to split the libra ...
paired-end sequencing demultiplex dual primers written 2.2 years ago by kristjan110 • updated 20 months ago by Brian Bushnell15k
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Answer: A: Download All The Bacterial Genomes From Ncbi
... NCBI has moved complete bacterial genomes file in their ftp site to ftp://ftp.ncbi.nih.gov/genomes/archive/old_refseq/Bacteria/ where it is not updated anymore. Do you know the reason? And how is it possible to download the most recent complete genomes as a whole fasta file? ...
written 2.4 years ago by kristjan110
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Submitting short reads to SRA
... Because many journals request to have all the sequences in a public database, I wanted to submit my data to ENA or GenBank, but now I have some problems. The sequencing was done in 2011 with Illumina HiSeq200 of 16S V6 region. After barcode and primer removal the average read length was about 80 bp. ...
database submission sra written 3.5 years ago by kristjan110 • updated 3.5 years ago by Ido Tamir4.9k
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Comment: C: Reference Database For Short Illumina Reads
... Our target was the V6 region. I have also tried RDP and CREST, but these gave more unclassified reads than mothur. But thanks for the new pipelines. I will try them out. ...
written 5.4 years ago by kristjan110
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Reference Database For Short Illumina Reads
... I am analysing soil samples that have been sequenced with Illumina HiSeq. After assembling paired end reads and denoising the average read length was about 80 bp. So far I have used Greengenes reference taxonomy for classification (in mothur software, method is knn), but these results are very inacc ...
illumina classification sequencing written 5.4 years ago by kristjan110 • updated 5.1 years ago by Biostar ♦♦ 20

Latest awards to kristjan

Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Download All The Bacterial Genomes From Ncbi
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Download All The Bacterial Genomes From Ncbi
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Reference Database For Short Illumina Reads
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Reference Database For Short Illumina Reads

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