Moderator: Arun

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Arun2.2k
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Posts by Arun

<prev • 312 results • page 1 of 32 • next >
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Mining condition specific gene expression data
... Hi, tl;dr version - How can we use Genevestigator to find out if the set of genes we've obtained from DGE analysis of our RNA-Seq data specific to a condition (biotic stress) are also induced in response to various other biotic stresses or not? We work with the model plant Arabidopsis thaliana. -- ...
data-mining microarray rna-seq written 3.2 years ago by Arun2.2k
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Comment: C: Obtaining "Gene-Association" File For Go Term Analysis
... I switched to MapMan software+annotations. ...
written 3.9 years ago by Arun2.2k
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Comment: C: Counting Reads On Paired-End Strand-Specific Rnaseq Data
... @MicheleBusby, DGE is differential gene expression and we're talking about paired-end RNA-sequencing with Illumina. mRNA is fragmented before converting to (c)DNA and further processing. There's no particular bias I am aware of, therefore, reg. one end always mapping poorly because it's from the Pol ...
written 4.2 years ago by Arun2.2k
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Counting Reads On Paired-End Strand-Specific Rnaseq Data
... Hello everybody, I've a strand-specific paired-end library on which I'd like to perform some standard DGE analysis. However I'm quite unclear about how to go about counting reads. Usually when I have a paired-end (unstranded) library, I first clip them for adapters and trim for quality. And when do ...
paired-end gene-expression strand rna-seq written 4.2 years ago by Arun2.2k • updated 4.2 years ago by Ashutosh Pandey11k
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Comment: C: Bringing Back Downvote
... Istvan, reg. your 2nd point, I've never seen the reputation go below 1 on SO. For your 1st point, the score for a question, if it's negative, is displayed as such. Usually such questions gets closed and stays so unless the question has been edited and is better and someone votes it to be reopened. T ...
written 4.3 years ago by Arun2.2k
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Comment: C: Bringing Back Downvote
... I would like to add just one point to Ih3's points. This is a Q and A website as opposed to a normal forum. So the questions are expected to be clear for someone who might search sometime later. And the quality of a question matters. And so does the quality of an answer. Part of dealing with a forum ...
written 4.3 years ago by Arun2.2k
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Comment: C: Filtering Genes For Differential Gene Expression Analysis
... Damian, thanks for your reply. Regarding your question, my objective is to reduce too many results with really low counts being DGE. For ex: if you were to do a glm.nb fit on reads from condition 1 = c(2,3,4) and condition 2 = c(30,22,25) and assume these reads come from a gene whose length is 2 Kb ...
written 4.3 years ago by Arun2.2k
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Filtering Genes For Differential Gene Expression Analysis
... Hello, I've samples under two different conditions (3 biological replicates each) that I'm about to analyse for differential gene expression. I've obtained read counts over all exons for each gene for all replicates. Now, I've always had trouble with filtering a set of genes which are "not expresse ...
rpkm deseq edger written 4.3 years ago by Arun2.2k • updated 4.3 years ago by Damian Kao14k
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Answer: A: Phd Candidate Interview Questions For A Mixed Lab/Bioinformatics Project
... I basically agree with Emily's answer. In addition, my recommendation would be to first ask what he/she has done and take it from there. For example, if someone has not worked at all on an NGS project, it doesn't make sense to ask them to explain the workflows (and there are/were quite some colleagu ...
written 4.3 years ago by Arun2.2k
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Comment: C: Upregulated And Downregulated Genes
... You can not know the "true" expression of the transcripts even though it's RNA-seq (at least not yet to my knowledge). What you've is the number of reads that map to the gene (either including or excluding introns). But it is not transcript expression. That's why it's called differential gene expres ...
written 4.5 years ago by Arun2.2k

Latest awards to Arun

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Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Deseq, Edger And Cuffdiff - Different Result
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