User: dmr210

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dmr2100
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Posts by dmr210

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Differential expression in samples where major gene is downregulated
... Hi, I have samples where one gene accounts for more than 40% of the total number of reads in normal conditions. In one phenotype that I consider, that gene is up-regulated. How will that impact the differential expression of the other genes? How does DESeq2 do the normalisation to avoid consideri ...
deseq2 written 6 months ago by dmr2100 • updated 6 months ago by Michael Love14k
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salmon quantification - identical transcripts in fasta file
... Hi, I am using Salmon to quantify transcript expression based on RNAseq. I am using the ensembl annotation, and as I am interested in non-coding RNA (lncRNA in particular) I merged the "cdna.all" and the "ncrna" fasta files. (see ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/) After loo ...
salmon written 7 months ago by dmr2100 • updated 7 months ago by James W. MacDonald45k
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Comment: C: GC/length bias correction in gene expression quantification - Is CQN necessary i
... Thanks very much for your very clear answer. I had decided to go for that option, but was really unsure as to whether I was making the right choice, and it is very reassuring to have an expert's opinion!  Would you change your answer if I specified that I am using single end data or does that not h ...
written 8 months ago by dmr2100
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GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
... Hi, Considering multiple RNA-seq samples for which we are interested in gene expression quantification, with the aim of using it for differential expression with DESeq2 and for eQTL analysis, what would be the best way to correct for GC content bias and transcript length bias? I have previously us ...
rnaseq cqn deseq2 salmon tximport written 8 months ago by dmr2100 • updated 8 months ago by Michael Love14k

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