User: piet

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piet1.7k
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Posts by piet

<prev • 207 results • page 1 of 21 • next >
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Comment: C: Bbduk filters away good reads
... > I believe, this can be confusing This is not confusing at all. Please make yourself familiar with the mathematics of Q values. Q values represent a logarithmic transformation of the error rates. Logarithmic transformations are often used in science and engineering, but have some pit falls, e ...
written 5 weeks ago by piet1.7k
2
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Answer: A: Phylogenomic tree construction
... > construct phylogenomic tree using the whole genome of certain bacterial strains I would advise not to use whole genomes for phylogeny. You should restrict your analysis to highly conserved genes from the core genome and you should exclude repeats and sites which presumably have arisen by any k ...
written 5 weeks ago by piet1.7k
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Answer: A: Microbiome Taxonomy composition
... > exaplanations? Contamination. ...
written 6 weeks ago by piet1.7k
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Comment: C: SRA files bulk downloads
... This means, that download has finished successfully. Please note that SRA files are not self contained. This particular SRA file comprises a mapping of the reads to reference sequence AL123456.2 (isolate H37Rv). This reference sequence was also downloaded to your local disc. The following command wi ...
written 7 months ago by piet1.7k
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Answer: A: Sequence reads and complete assembly
... Only few people submit their reads as well as their assemblies. SAMN04994921 is a nice example where both, a set of Illumina reads and a set of 25 contigs are available. https://www.ncbi.nlm.nih.gov/biosample/SAMN04994921 https://www.ncbi.nlm.nih.gov/sra/SRR3528286 https://www.ncbi.nlm.nih.gov/Tr ...
written 7 months ago by piet1.7k
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Answer: A: NCBI Entrez not returning the correct DNA sequence for all entries
... > dnahandle= Entrez.efetch(db = "nuccore", id=dnaacc,rettype="fasta",retmode="txt",seq_start=start1,seq_stop=stop1) You are passing the "accession" to "id". While accession is an alphanumerical string, the id is a pure number. The id of the "nuccore" table is also called GI. In NCBI Genbank, suc ...
written 8 months ago by piet1.7k
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Comment: C: cutadapt error problem
... > cutadapt -b /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/file:barcodes.fasta > -o /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq.gz input > /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/Pool1_S1_L001_R1_001.fastq try to remove the word "input" from y ...
written 8 months ago by piet1.7k
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Comment: C: de novo assembly of circular plasmid
... > annotate the plasmid, how can I do that? If you do not have experience with software for annotation yet, then I would recommend that you do it manually as an exercise. This short plasmid presumably has 10 to 15 genes, thus manual annotation is feasible. First determine the open reading fra ...
written 8 months ago by piet1.7k
0
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Comment: C: de novo assembly of circular plasmid
... > the average per base coverage I do not mean the average coverage. Please evaluate if there is any sharp drop in coverage along the sequence except for the ends. Map the reads to pTPK_AAV2 and then visually inspect the BAM file with Tablet and also run bedtools genomecov on the BAM file. ...
written 8 months ago by piet1.7k
0
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Answer: A: de novo assembly of circular plasmid
... The gap indicates that your putative plasmidic contig differs from pTPK_AAV2 by a deletion of about 500 nt. Such deletions or other recombinations are commen in plasmids. You should annotate pTPK_AAV2 and check if lost of the gap region is plausible. To verify the gap, you may map your reads to pTKP ...
written 8 months ago by piet1.7k

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Scholar 5 weeks ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 5 weeks ago, created an answer that has been accepted. For A: Where to put start for assembled genome/plasmid
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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
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