User: lu.ne

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lu.ne50
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Posts by lu.ne

<prev • 16 results • page 1 of 2 • next >
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RNA-Seq with 4 conditions - Analysis design choice with DESeq2
... Hi, I've been trying to look at differential expression in 33 samples (design file below) with DESeq2 in R and I am unsure about the best way to analyse it. sample line drug disease time A1 A Yes No 3 A2 A Yes No ...
R rna-seq written 4 weeks ago by lu.ne50
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Comment: C: RNA-Seq time-series analysis among disease samples - analysis strategy advice
... Hi Akos, I have not found anything I'm afraid (that's probably because they did not intend the tool to be used in that kind of situations though). ...
written 5 weeks ago by lu.ne50
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Comment: C: RNA-Seq time-series analysis among disease samples - analysis strategy advice
... Thanks a lot for the input, that's helpful. ...
written 10 weeks ago by lu.ne50
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Comment: C: RNA-Seq time-series analysis among disease samples - analysis strategy advice
... Sure, sorry if this was not clear, I'll edit accordingly. The replicates are actually the 200 patients, the samples are from whole blood and are collected on patients with arthritis (from when they were 'diagnosed' and then four other times with 6 months between each one of the samples). There are h ...
written 11 weeks ago by lu.ne50
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RNA-Seq time-series analysis among disease samples - analysis strategy advice
... Hi, I've been trying to perform some time-series analysis (identification of genes with non-constant expression over time, clustering of genes given their trend over time...) of RNA-Seq data (counts obtained from featureCounts) for a group of 200 patients with arthritis, all sampled at 5 different ...
time-series rna-seq written 11 weeks ago by lu.ne50 • updated 11 weeks ago by kristoffer.vittingseerup1.4k
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Comment: C: RNA-Seq data, batch effect source
... Ok, makes sense, thanks for the answer, it sure gives me ideas for what to do next! ...
written 18 months ago by lu.ne50
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RNA-Seq data, batch effect source
... Hi All, I am currently trying to normalise some RNA-Seq data. Indeed, samples came from two different batches and when plotting the values using a PCA plot the separation is clearly marked. It seems that the protocol used for samples processing is the same as well as the lab where the analyses wer ...
rna-seq written 18 months ago by lu.ne50 • updated 18 months ago by Devon Ryan88k
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Comment: C: RNA-Seq pipeline for clustering
... It seems to be working just fine with featureCounts, thanks! ...
written 21 months ago by lu.ne50
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Answer: A: OrthoMCL step 12: [mclxReadDimensions] could not parse header
... Assuming your file is in abc format (A B weight, a line for each pair) then you might want to add --abc at the end of your command, I had a similar error when using mcl in the past and it was because of this omission. ...
written 21 months ago by lu.ne50
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RNA-Seq pipeline for clustering
... Hi All, I am currently performing RNA-Seq data analysis, the aim is to cluster individuals and so far I have been using this pipeline to obtain expression values (using reference and gtf files GRCh38.86): - cutadapt - STAR - cufflinks, using this command: `cufflinks -p 24 -o output_folder_path -g p ...
rna-seq written 21 months ago by lu.ne50 • updated 21 months ago by MMa250

Latest awards to lu.ne

Popular Question 17 months ago, created a question with more than 1,000 views. For STAR - genome indexes generation, genome file not created
Scholar 21 months ago, created an answer that has been accepted. For A: OrthoMCL step 12: [mclxReadDimensions] could not parse header

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