User: piet

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piet1.6k
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Posts by piet

<prev • 204 results • page 1 of 21 • next >
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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 3 months ago by piet1.6k
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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 3 months ago by piet1.6k
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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 4 months ago by piet1.6k
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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 4 months ago by piet1.6k
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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 4 months ago by piet1.6k
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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 4 months ago by piet1.6k
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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 4 months ago by piet1.6k
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Comment: C: How can I submit paired-end SRA data to NCBI?
... gzip each file separately and submit as two files ...
written 5 months ago by piet1.6k
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Comment: C: command-line tool to split genome FASTA into equal chunks?
... > BioPython script but I would like something faster then write it in plain python ...
written 5 months ago by piet1.6k
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Comment: C: Sra-toolkit: Prefetch error
... I have tested it, and it worked fine for me. Unfortunately, there is a typo in my answer, please try without the backtick. > prefetch SRR7768518 ...
written 5 months ago by piet1.6k

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Teacher 11 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
Appreciated 3 months ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
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