User: Sethzard

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Sethzard10
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Posts by Sethzard

<prev • 13 results • page 1 of 2 • next >
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Align to inserted sequence
... We have some RNA from knock-in mice, there are two different sequences we're looking for. What is the best way to check for their presence? Should I just turn them into a sequence and use them as the reference genome for STAR or something to align to? Is there a way I can easily incorporate it into ...
alignment rna-seq written 29 days ago by Sethzard10
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Comment: C: How to setup a Summarized Experiment
... That worked, and also worked with adding colData=Support. I think I got confused because the command that's listed didn't work: SummarizedExperiment(assays=list(counts=counts), colData=colData) Sorry if I missed something, but it didn't seem obvious. ...
written 16 months ago by Sethzard10
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How to setup a Summarized Experiment
... I'm starting from a count matrix called Raw Dreads with each column being an RNA-Seq dataset, and each row being the reads associated with a gene (the names are EnsemblIDs). I've also created matrix called support with the columns: sample, the name of an RNA-Seq dataset, and condition, which is th ...
summarized experiment enrichment browser rna-seq R written 16 months ago by Sethzard10
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Multiple DESeq2 comparisons
... I have multiple conditions each with multiple mutants and their own wild types. Each sample has been sequenced using 2 different methods. I've been trying to work out if it's feasible to compare samples to their wildtypes then do a comparison between comparisons. Currently, I've been using contras ...
R deseq2 rna-seq written 24 months ago by Sethzard10
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What do 0s in stageR mean?
... I'm running stageR as part of a pipeline based on DRIMSeq and wanted to know what it means when the transcript level padj is equal to 0, particularly when the gene is non-significant. I'm pretty sure that in some cases if the padj is 0 it means that the chance of it being different due to chance is ...
stager R rna-seq written 3.0 years ago by Sethzard10
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Comment: C: Creating a targets matrix
... I have read that manual so many times yet somehow passed over that bit. THANK YOU! ...
written 3.8 years ago by Sethzard10
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Comment: C: Creating a targets matrix
... I've seen that post, which is why I'm not trying to voom it. I'm trying to use the Log2 scale as he suggested and I've run face first into a wall. ...
written 3.8 years ago by Sethzard10
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Comment: C: Creating a targets matrix
... We don't have the library size given to us. By have the library size do you mean calculate the library size from the lengths of each sequence? And thanks :) ...
written 3.8 years ago by Sethzard10
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Comment: C: Creating a targets matrix
... Sadly I am all too aware that it's suboptimal but he's said that that's what he wants us to use. I've seen a few places you can use a set of logged scores in Limma like [here][1] but I'm struggling to work out how to do it with what we've been given. [1]: https://support.bioconductor.org/p/5627 ...
written 3.8 years ago by Sethzard10
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Creating a targets matrix
... As part of a group software development project we have been given 9 sets (3 sample types each containing 3 replicates) of assembled bat transcriptome sequences and their FPKM scores. The samples are the bats before being infected, 8 hours after being infected and 24 hours after being infected. The ...
limma rna-seq written 3.8 years ago by Sethzard10 • updated 3.8 years ago by theobroma221.1k

Latest awards to Sethzard

Popular Question 15 months ago, created a question with more than 1,000 views. For blastn biopython error: positional arguments
Popular Question 16 months ago, created a question with more than 1,000 views. For Creating a targets matrix

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