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 6 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 6 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 6 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 6 months ago by andrewpountain0 • updated 6 months ago by Martin Morgan ♦♦ 22k

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