User: bioinform

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bioinform20
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Posts by bioinform

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Comment: C: Is there any open source Python bacterial GWAS-based software and a tutorial to
... Bacterial GWAS.......... ...
written 19 months ago by bioinform20
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(Closed) How practically to produce a whole genome contig from the short reads of M tuberculosis?
... How practically to produce a whole genome contig from the short reads of M tuberculosis? How many of short reads are required if they are from the online database or from the local sequencing machine? Is a pair of fastqs enough to make a contig? ...
tuberculosis contig written 19 months ago by bioinform20
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(Closed) Is there any open source Python bacterial GWAS-based software and a tutorial to learn on an example?
... Is there any open source Python bacterial GWAS-based software and a tutorial to learn on an example? Need an example with a readable clean and documented codes. Want to find a software example where VCFs are converted to a 0/1 matrix and phenotype matrix is created from the web-hosted XML data. Then ...
software gwas association written 19 months ago by bioinform20
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Where and how to fetch phenotype data of the relevant SRA-identified tuberculosis WGS samples?
... Where and how to fetch phenotype data of the relevant SRA-identified tuberculosis WGS samples? I am developing GWAS-based software, want to fetch pehnotype data from web, all the relevant available information to the fastqs I have. Is that information available for a single WGS sample and in what f ...
software sra association gwas written 19 months ago by bioinform20 • updated 19 months ago by Istvan Albert ♦♦ 79k
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Answer: A: Is it possible to download Neisseria Meningitidis whole gneomes using fastq-dump
... found on my own at https://www.ncbi.nlm.nih.gov/sra/?term=meningococcus ...
written 19 months ago by bioinform20
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(Closed) Is it possible to download Neisseria Meningitidis whole gneomes using fastq-dump from SRAToolkit?
... Is it possible to download Neisseria Meningitidis whole gneomes using fastq-dump from SRAToolkit? Looking for SRA identifiers of N. meningitis short reads, fastq files. ...
sratoolkit fastq-dump neisseria sra written 19 months ago by bioinform20
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(Closed) What software can accept a vcf and and a matrix of pheotype features to do bacterial GWAS?
... What software can accept a vcf and and a matrix of phenotype features to do bacterial GWAS? ...
gwas written 19 months ago by bioinform20
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Comment: C: How to run linksBed function from the Bedtools on a M. tuberculosis gene set?
... do you know how to run linksBed function for a tuberculosis genes? what -org should be and database referenced? ...
written 19 months ago by bioinform20
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(Closed) How to run linksBed function from the Bedtools on a M. tuberculosis gene set?
... Code linksBed -i -org mycobacteria g1.bed > links2bed.html does not work g1.bed contains AL123456 5123 7267 gyrB AL123456 7302 9818 gyrA AL123456 759808 763325 rpoB How to run linksBed function ...
bedtools tuberculosis links written 19 months ago by bioinform20
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Comment: C: Is it possible to run variant calling software in parallel, are there any Shell
... need a code example using GNU parallel ...
written 19 months ago by bioinform20

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