User: lu.ne
lu.ne • 50
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Posts by lu.ne
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... 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 ...
written 6 months ago by
lu.ne • 50
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... 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 6 months ago by
lu.ne • 50
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... Thanks a lot for the input, that's helpful. ...
written 7 months ago by
lu.ne • 50
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... 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 7 months ago by
lu.ne • 50
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... 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 ...
written 7 months ago by
lu.ne • 50
• updated
7 months ago by
kristoffer.vittingseerup • 2.0k
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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 23 months ago by
lu.ne • 50
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... 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 ...
written 23 months ago by
lu.ne • 50
• updated
23 months ago by
Devon Ryan ♦ 91k
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Comment:
C: RNA-Seq pipeline for clustering
... It seems to be working just fine with featureCounts, thanks! ...
written 2.2 years ago by
lu.ne • 50
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... 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 2.2 years ago by
lu.ne • 50
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... 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 ...
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For STAR - genome indexes generation, genome file not created
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For A: OrthoMCL step 12: [mclxReadDimensions] could not parse header
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