User: fengzys

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fengzys50
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Posts by fengzys

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Answer: A: How to retrieve all fasta sequences using Assembly/BioProject ID using Entrez Pr
... Thanks, however, I found batchentrez can not deal with these master record as well. e.g. genome id 44851 44849 44848 or assembly 739291 738621 194461 or gi 1027168540 1027763052 738803256 ...
written 3.1 years ago by fengzys50
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How to retrieve all fasta sequences using Assembly/BioProject ID using Entrez Programming Utilities
... I am trying to download all the viral and bacterial genome (in Genome database), I have used Entrez utilities. Firstly, Esearch was use to retrieve all the viral Genome UID, which was then translated to nuccore gi number by Elink, some gi number corresponds to the parental description of a WGS proje ...
utilities ncbi efetch written 3.1 years ago by fengzys50
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How to automatically annotate the SNP by GenBank info?
... I have some newly sequenced EBV genome, I would like to find all SNPs and their annotation (e.g. which gene, whether synonymous or non-synonymous) by aligning the genome to reference derived from GenBank, any software available for doing this? Thanks. ...
annotation genbank written 3.2 years ago by fengzys50
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What happens to this gene?
... I found many reads mapped to a gene in a wired way, any suggestion on what happens here? Assuming the gene has sequence: ABCDEFGHIJK Its complement are abcdefghijk The reads are like: kjihgABCDEF What kind of chromosome rearrangement could produce this? or artifacts? ...
chromosome transversion written 3.3 years ago by fengzys50 • updated 3.3 years ago by John12k
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Answer: A: How to obtain the strand information from DNA-seq data
... After some searching and reading, I understand that the oligo immobilised on the flow cell are P7 and P5 with some extra sequences and chemical modification. thus I guess both template DNA with P7 complement and P5 complement could be attached to the flow cell, though the one that synthesized on P7 ...
written 3.3 years ago by fengzys50
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Comment: A: How to obtain the strand information from DNA-seq data
... To Devon Ryan, I am planing to ask them, for my understanding, if no PCR was done during the library preparation, the strand information should be kept. I have a library with PCR after hybridization enrichment(using P7,P5 primers), I don't know if strand information is kept or not. By the way, du ...
written 3.3 years ago by fengzys50
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Comment: A: How to obtain the strand information from DNA-seq data
... ADD REPLY does not work for me know. The paper studying strand-specific mutation pattern is http://www.ncbi.nlm.nih.gov/pubmed/25271376, they did not mention how this was done. ...
written 3.3 years ago by fengzys50
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How to obtain the strand information from DNA-seq data
... I have been confused on how to obtain the strand information from mapping result. In a paper, the authors have calculated the mutation rate on sense strand and antisense strand by using WGS sequencing data( to study somatic mutation),for my understanding, the strand information should be derived fro ...
strand written 3.3 years ago by fengzys50

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