User: andrewpountain

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Posts by andrewpountain

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Comment: C: Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
... Thanks for clarifying! Andrew ...
written 17 months ago by andrewpountain0
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Comment: C: Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
... Hi Mike, Thanks for getting back to me. I haven't looked at SNP frequency, it's my first time working with these genomes. I think there's a reasonable amount of divergence between haplotypes but haven't quantified. Something to look into. My feeling is that the genes that are substantially underest ...
written 17 months ago by andrewpountain0
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Comment: C: Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
... Hi Ryan, Thanks for your response. Yes that's definitely worth a try to compare. I'm assuming the tx2gene functionality in tximport just sums alternative transcripts for the final gene count, I'll check up on this. Thanks, Andrew ...
written 17 months ago by andrewpountain0
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Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
... Hi there, I'm using DESeq2 for analysis on salmon-derived counts. It's a bit of a niche question, but advice would be appreciated. I am trying to compare expression of orthologous genes across multiple closely related species (obviously taking care over the various pitfalls that entails). One issu ...
deseq2 salmon written 17 months ago by andrewpountain0 • updated 17 months ago by Martin Morgan ♦♦ 23k

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