User: jdhindsa1999

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Posts by jdhindsa1999

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Comment: C: DESeq multiple factor question
... Thank you very much for the help! I've manually edited my matrix and then provided it to DESeq. I reordered my genotypes using `ddsHTSeq_filtered$Genotype <- factor(ddsHTSeq_filtered$Genotype, levels = c("WT", "mdx", "d52"))` Now my question remains in extracting the relevant contrasts, as you ...
written 8 days ago by jdhindsa19990
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Comment: C: DESeq multiple factor question
... Thank you all for the help! Do you have any suggestions on how to analyze the data given that I don't have d52 p8? Should I do the analysis separately for the p8 and then analyze the 6m and 12m together? ...
written 12 days ago by jdhindsa19990
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Comment: C: DESeq multiple factor question
... Thank you for the help. However, when I try to include the interaction term, I get an error saying that the model matrix is not full rank. Do you know if this is an issue with the way the experiment was designed? I am attaching an image of my samples. [samples][1] ![enter image description here][2] ...
written 12 days ago by jdhindsa19990 • updated 12 days ago by GenoMax96k
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DESeq multiple factor question
... Hi, This is my first time using the DESeq2 package for RNA-seq analysis. I am analyzing a longitudinal study of three different time points in mice, with three different genotypes of animals - 1 wildtype, 2 mutated. I want to evaluate differential expression as an effect of the different genotypes ...
R differential-expression rna-seq sequencing written 12 days ago by jdhindsa19990 • updated 12 days ago by Carlo Yague5.7k
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Comment: C: Help with STAR aligner for multiple 50 bp PE samples
... Thanks so much for the help! Would the ls command be appropriate instead of the find command? ...
written 28 days ago by jdhindsa19990
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Help with STAR aligner for multiple 50 bp PE samples
... Hello, I am new to RNA-seq analysis, and I am attempting to align my sequence reads to my indexed genome in STAR (I've already indexed the genome). I have 50 samples in total, and each sample has 4 respective fastq.gz files – this was PE with 50 bp reads, and run in two lanes. Thus, per sample, 2 ...
alignment star rna-seq written 28 days ago by jdhindsa19990

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