User: piet

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piet1.7k
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Posts by piet

<prev • 208 results • page 1 of 21 • next >
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Answer: A: Multiple Sequence Alignment for >20 Sequences
... My preferred multi sequence aligner for the command line is mafft nowadays. The rabies virus has a genome size about 12000 nt. It should be feasible to align > 20 whole genomes with mafft on an standard PC, maybe within 10 minutes or less. ...
written 12 months ago by piet1.7k
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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 14 months ago by piet1.7k
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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 14 months ago by piet1.7k
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Answer: A: Microbiome Taxonomy composition
... > exaplanations? Contamination. ...
written 14 months 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 20 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 20 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 20 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 21 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 21 months ago by piet1.7k
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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 21 months ago by piet1.7k

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Great Question 13 months ago, created a question with more than 5,000 views. For Howto use NCBI programs behind a HTTP proxy
Scholar 14 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 14 months ago, created an answer that has been accepted. For A: Where to put start for assembled genome/plasmid
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Python Programming (Suggestions are needed)
Teacher 14 months 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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Appreciated 19 months ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
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