User: pthom010

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pthom0100
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Posts by pthom010

<prev • 32 results • page 2 of 4 • next >
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Construct Heatmap and Cut Clusters
... I have a dds DESeq object with 30 samples and about 8000 DEGs I would like to look at in a heatmap by cutting it into x clusters and having all x clusters on the same heatmap. I was able to make the following figure with ComplexHeatmap: https://ibb.co/G21bpCw [Heatmap with 8000 DEGs Clustered u ...
R rna-seq written 5 months ago by pthom0100
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Comment: C: Heatmap with VST Normailzed Data
... Thank you. I ended up getting to the root of the problem and I can produce the heatmap now. However, I will read these tutorials because ComplexHeatmap looks rather impressive. Thanks! ...
written 5 months ago by pthom0100
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Heatmap with VST Normailzed Data
... I conducted a time-course with 5 time points and two samples (three replicates for each time point).I have a dds object with 30 columns( one for each replicate) that I have vst-transformed. I have my columns as samples and my rows as transcripts. I have about 8000 DEGs and would like to make a heatm ...
R rna-seq written 5 months ago by pthom0100
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Comment: C: DESeq2 Pre-filtering and Subsetting
... That works. Thanks!!! ...
written 5 months ago by pthom0100
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Comment: C: DESeq2 Pre-filtering and Subsetting
... My apologies. My dds variable is two plant genotypes over a period of time and each sample 1 - 30 in my dds object belongs to a genotype. Columns 1 - 15 belong to one genotype (Three replicates for 5 time points) and columns 16 - 30 belong to another. What I would like to do is row means filter by t ...
written 5 months ago by pthom0100
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Comment: C: DESeq2 Pre-filtering and Subsetting
... Thanks but I wanted to filter the row means by treatment (only filtering out those with row means less than 30 between samples 1 - 15 and 16-30, separately). Would I just do: dds_30 <- dds[rowMeans(counts(dds)[, 1:15;16:30]) >= 30, ] ...
written 5 months ago by pthom0100
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DESeq2 Pre-filtering and Subsetting
... I have a dds object in DEseq2 and I wanted to do row means filtering on my object. I have 30 total samples, therefore I have 30 total columns in the count table. I'd like to filter all read counts lower than 30 for each treatment (for rows 1-15 and rows 16-30). I've tried the following code: ke ...
R rna-seq written 5 months ago by pthom0100 • updated 5 months ago by rpolicastro3.1k
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Reducing De Novo Reads
... I recently completed a de novo sequencing project and want to do DE analysis on my reads. I would like to remove duplicate reads from my transcriptome and was wondering if anybody had any suggestions for software to use. I'm aware of CD-HIT and iAssembler but was curious if there was anything else o ...
assembly linux R sequencing written 7 months ago by pthom0100
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Comment: C: DESeq2 on a Novel Organism
... I'm honestly very confused. Someone told me I could just customize the R scripts that Trinity uses but that would require a significant amount of customizing all of the R scripts (filtering of row means by genotype, specific FDR and FCs). I think it might be more efficient to run the analysis in DES ...
written 7 months ago by pthom0100
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DESeq2 on a Novel Organism
... I have a series of reads from an organism that has not been sequenced or annotated. I am using DESeq2 (through R) to do a differential expression analysis on my genes and was wondering if it was feasible to annotate them using a tx2gene file with Gene IDs in the third column? Theoretically, I would ...
R deseq2 rna-seq written 7 months ago by pthom0100

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