User: michael.nagle

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michael.nagle100
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Posts by michael.nagle

<prev • 38 results • page 1 of 4 • next >
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Comment: C: vcf2bed giving empty bed file as output
... I didn't figure out the cause of the problem, so I used PLINK to convert the VCF to bed instead of using vcf2bed. It's very easy with PLINK. https://bioinformatics.stackexchange.com/questions/3667/converting-vcf-file-to-plink-bed-bim-fam-files ...
written 5 months ago by michael.nagle100
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Comment: C: Confounding factors when comparing effects of expression between RNA-seq samples
... I'm working on a proposal for possible future research and trying to make the most of available resources and a limited budget. There's no reason we can't perform both qPCR and RNA-seq for some number of samples in Sample A. It is possible for us to find enough samples in Sample A without SNPs that ...
written 9 months ago by michael.nagle100
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Confounding factors when comparing effects of expression between RNA-seq samples and qPCR samples?
... I'm trying to design an experiment comparing the effects of various expression levels of Gene X between Sample A and Sample B. If measurements in Gene X expression are from RNA-seq in Sample A and qPCR in Sample B, what assumptions must be made in comparing the effects of expression on a trait betwe ...
qrtpcr transcriptomics rna-seq qpcr expression written 9 months ago by michael.nagle100 • updated 9 months ago by Devon Ryan94k
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Job: REU / Research Experience for Undergraduate in genomic plant biology available at Oregon State University in Corvallis
... A position is available for summer 2019 working in an NSF-funded project to identify the genes and mechanisms that control plant regeneration and transformation capacity. See these links for project [summary][1] and [background][2]. Position duties are described [here][3] (biological science posit ...
bioinformatics genetics job genomics plant written 11 months ago by michael.nagle100
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... My VCF is in VCF format, but for the purpose of this post I opened it in a spreadsheet program and took a screenshot so that it would be human-readable. This bcftools command would work if indels were called in this VCF. As you can see in the screenshot, only SNPs have been called. My question is a ...
written 11 months ago by michael.nagle100
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... I've edited my post to include a sample of the VCF file. Thanks. ...
written 11 months ago by michael.nagle100
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... No, I'm working with a non-model plant organism. ...
written 11 months ago by michael.nagle100
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Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... A number of SNPs appear to be associated with a trait of interest. I wish to look into all of these SNPs and get an idea of how they affect genes and whether they correspond to insertions or deletion mutations (indels). I do not have access to genome sequence data for the GWAS population, only SNP ...
gwas written 11 months ago by michael.nagle100 • updated 9 months ago by Biostar ♦♦ 20
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GWAS: Same workflow and inputs, different servers, very different output (EMMAX)
... Using our server, I'm trying to replicate collaborators' results using the same workflow and dataset used on their server. This is the standard EMMAX workflow detailed here: https://genome.sph.umich.edu/wiki/EMMAX For some reason, results are very different. One server seems to produce nothing but ...
server gwas C cluster emmax written 21 months ago by michael.nagle100
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Comment: C: Extra header column stopping EMMAX (C), but not seen in input files
... This one-liner says the input files are tab-delimited and I also made sure by replacing all tabs with $ and by double checking the perl code used to format the tab-delimited input files. ...
written 24 months ago by michael.nagle100

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Popular Question 9 months ago, created a question with more than 1,000 views. For In new genome, how is it decided which strand is forward/reverse?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to BLAST 400 genes against genome at once?
Popular Question 11 months ago, created a question with more than 1,000 views. For In new genome, how is it decided which strand is forward/reverse?
Popular Question 20 months ago, created a question with more than 1,000 views. For Trying to compare 3 versions of genome in IGV but can't sort in IGVtools or Samtools
Popular Question 20 months ago, created a question with more than 1,000 views. For In new genome, how is it decided which strand is forward/reverse?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to BLAST 400 genes against genome at once?
Appreciated 3.5 years ago, created a post with more than 5 votes. For In new genome, how is it decided which strand is forward/reverse?
Good Question 3.5 years ago, asked a question that was upvoted at least 5 times. For In new genome, how is it decided which strand is forward/reverse?
Student 3.5 years ago, asked a question with at least 3 up-votes. For In new genome, how is it decided which strand is forward/reverse?

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