User: Macspider

gravatar for Macspider
Macspider1.5k
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Vienna - BOKU
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macspider_music
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Posts by Macspider

<prev • 323 results • page 1 of 33 • next >
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Comment: C: Which package to use for RPKM/FPKM RNA-seq counts?
... As far as I know, you can plug FPKM values in. ...
written 3 hours ago by Macspider1.5k
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Comment: C: Technical replicates in RNAseq
... I couldn't agree more. Basically, on the theoretical level I agree with @WouterDeCoster but on the practical level I don't because I saw what @grant.hovhannisyan said happen. ...
written 3 days ago by Macspider1.5k
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Comment: C: Technical replicates in RNAseq
... > For our experiment we need to reach 20mln reads depth for a given sample I think, if the funding allows you to do it, making a 20 million reads run is better. When in one year you'll be sending the paper, the revisors could easily asked you 1) why did you sum the read counts 2) why did you seq ...
written 3 days ago by Macspider1.5k
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Comment: C: Technical replicates in RNAseq
... How are you losing on it? - if you are sequencing the same sample twice in the same run, the two replicates should have the same sequencing depth - if you are sequencing the same sample once again in a different run, you might have different sequencing depths for different runs according to you ...
written 3 days ago by Macspider1.5k
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Comment: C: Technical replicates in RNAseq
... But the amount of sequenced reads has to be connected to the amount of transcripts that you have in your sample, which ultimately defines the expression concept. To me, adding technical replicates means logically taking the transcripts of the same sample twice. I totally get your point, I'm more on ...
written 3 days ago by Macspider1.5k
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Comment: C: Technical replicates in RNAseq
... There are two equally respectable opinions, the ones that we just brought up. I gave you detailed explanation for my opinion, I am truly convinced of what I say. But I am eager to hear the reasons for which you *could* add them, perhaps I can change my mind if provided with enough evidence (ain't th ...
written 3 days ago by Macspider1.5k
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Comment: C: Technical replicates in RNAseq
... Wouter has more biostars points, I am not going against moderators :-P ...
written 3 days ago by Macspider1.5k
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Comment: C: GFF3 file incompatibilities (source: BRAD)
... The "parent" is missing, probably a gene, as @Juke-34 says. ...
written 3 days ago by Macspider1.5k
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Answer: A: Which package to use for RPKM/FPKM RNA-seq counts?
... > which package in R should i use for Differential gene expression? Assuming you mean to do diff.expr. with FPKM, I think Limma does a pretty good job. However ... > among many packages which package is better? This question I think is hard to answer. The jury is out on this one! > is ...
written 3 days ago by Macspider1.5k
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Answer: A: Technical replicates in RNAseq
... My 2 cents: no, it's very bad practice to do that. Detailed explanation: technical replicates are different RNASeq runs performed on the same sample, they have to be *averaged*. You are taking a snapshot of the transcriptional profile of your sample, and you're sequencing it twice to avoid biases ...
written 3 days ago by Macspider1.5k

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 4 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 4 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Scholar 4 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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