User: csijst

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csijst0
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Posts by csijst

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Understanding data output of sailfish-cir
... Hi, I am trying to use the sailfish-cir to quantify circular RNAs in my samples. I ran my paired ended RNAseq samples through BWA-mem and subsequently CIRI. Lastly, I parse it through sailfish-cir. I have a problem trying to interpret the information. In CIRI’s output, it displays information is i ...
ciri sailfish-cir written 18 months ago by csijst0
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Comment: C: Inconsistent RNAseq data in knockdown expt
... Hi Dr Peter, I am not that familiar with statistics, but do you mind explaining what do you mean by "larger number of tests"? Do you mean if I am interested in gene A (as compared to controls) but also interested whether gene B (or others) has a correlated change as stated in the log2foldchange (at ...
written 19 months ago by csijst0
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Comment: A: Inconsistent RNAseq data in knockdown expt
... Dear Dr Michael, My colleague and I didn't use plotCounts() but we checked the counts using counts['gene',]. So what you mean is (as far as you can understand) the data is true and it's probably not something related to the programming? I have some suspicion about the benchwork though. I do apprec ...
written 19 months ago by csijst0
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Comment: A: Likeliness Ratio Test
... Hi Dr Michael, Thank you! I had the same feeling initially. Because the algorithm is fixed. It's almost like saying 3 + 2 and 2 + 3, if I "reduce" 3, I'd still get 2. But I was reading in some sites (Bioconductor online manual - Likeliness Ratio Test section; DGE analysis - time course analysis se ...
written 19 months ago by csijst0
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Likeliness Ratio Test
... Hi, I understand the explanation when we set the design as ~ cell + dex, in which, we want to study the difference between dex treatment among cells. After which, a reduction (in the model) would be done for cell. But I find it hard to understand how will the program (with a fixed algorithm) will b ...
deseq2 design and contrast matrix written 19 months ago by csijst0
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Inconsistent RNAseq data in knockdown expt
... Hi, I am helping a colleague to conduct a differential expression analysis with RNAseq data but I have some concerns about the expression levels stated in the analysis. Based on the design of the experiment, my colleague states that protein A controls the stability of protein B; when prot A is redu ...
deseq2 written 19 months ago by csijst0 • updated 19 months ago by Peter Langfelder2.3k
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Pipeline to find Kozak sequence in RNAseq data and in silico translation
... Hi, Does anyone know how do I go about finding RNA sequences that contain the Kozak sequence in RNAseq data? And out of these RNA sequences, to do an in silico translation to peptide sequences? If you do have an article or pipeline that could guide me, do you mind sharing it with me? Thank you. R ...
rna-seq written 20 months ago by csijst0
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Comment: C: DESeq2 - DESeqDatasetFromMatrix
... Thank you. Do you happen to know whether there is any software that is able to conduct analysis for the said situation? I know it may not be statistically sound, but this analysis is not going to be used for publishing, rather, merely for information of any potential genes so that we can carry on wi ...
written 20 months ago by csijst0
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Comment: C: DESeq2 - DESeqDatasetFromMatrix
... Hi, Thank you for your time. I don't fully understand what you mean by being able to "compare treated (shRNA 1 and 2) to untreated (control)". As in, I'm not exactly sure how to go about doing it. Do you mean: design_shrna=data.frame(treatment=c("untr", "tr", "tr")) dds <- DESeqDataSetFromMatr ...
written 20 months ago by csijst0
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DESeq2 - DESeqDatasetFromMatrix
... Hi, I have some RNAseq data from a peer. She only has three conditions - control, shRNA1 and shRNA2; shRNA1 or 2 means two independent experiments to introduce the shRNA to cells, and test for knockdown of genes. Unfortunately, she did not conduct a replicate. I.e., I only have three datasets for D ...
deseq2 written 20 months ago by csijst0 • updated 20 months ago by Michael Love26k

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Popular Question 8 months ago, created a question with more than 1,000 views. For DESeq2 - DESeqDatasetFromMatrix

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