User: biostar.anon

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Posts by biostar.anon

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Comment: A: Uneven PCR in RNA-seq Preparation
... Yes while it is true that there's a protocole, I am currently in contact with a sequencing facility which states their standard method for if a DNA converted mRNA has too little molarity/ [] in QC is to amplify 5 supplementary cycle. Has anyone heard any similar protocol ? ...
written 10 months ago by biostar.anon0
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Uneven PCR in RNA-seq Preparation
... Is it normal practice to prepare mRNA-seq libraries with uneven PCR to compensate for low RNA input ? and if so how is it treated in analysis and communicated in article ? ...
rna-seq written 10 months ago by biostar.anon0
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Comment: C: what are the rules to simulate an Intermediate specimen ?
... Yes, the aim of this analysis is to test if a gene is outside the bounds of a linear intermediate of the two categories. ...
written 13 months ago by biostar.anon0
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what are the rules to simulate an Intermediate specimen ?
... Hi, The current question are about simulating counts or pseudo count table for individuals of an intermediate condition, to test the linearity of the response to the phenomenon. For example : Having 4 specimen condition at 0, 4 conditioned at 1, and several conditioned to known in between value wi ...
rna-seq written 13 months ago by biostar.anon0
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Comment: C: Poly(A) tail 5'/3' biais
... I am asking if a overabundance in poly(A) sequences (>1%) in RNA-seq data of a sample could be caused by RNA break during isolation (thus resulting in a 3' bias). I found a specimen file with an overabundance of A* sequences in fastqc compared all other specimens. Second, even when filtered for ...
written 2.0 years ago by biostar.anon0
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Poly(A) tail 5'/3' bias
... Is the abundance of Poly(A) tail (A^25), in sample isolated using poly-A mRNA, potentially caused by a 3' bias in the isolation ? Could using uneven specimen cause bias in analysis (even when filtered)? ...
rna-seq sequencing written 2.0 years ago by biostar.anon0 • updated 2.0 years ago by genomax76k
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RNAseq bad PCA, a differential expression analysis killer ?
... Hello, I was wondering is a bad or poor PCA (unclustered) a roadblock to a DEG analysis ? A colleague who had this problem recently suggested the interpretation that there is within this analysis variability (of course) but since each gene is tested separately they are still significantly over expre ...
rna-seq written 2.3 years ago by biostar.anon0 • updated 2.3 years ago by Devon Ryan93k
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Comment: C: RNAseq uneven PCR bias "how to take into best take into account uneven PCR bias
... but is there in your opinion a correct solution ? Is the batch effect integration an acceptable way in your opinion ? ...
written 2.3 years ago by biostar.anon0
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RNAseq uneven PCR bias "how to take into best take into account uneven PCR bias ?"
... Hello, I am a student doing a project with some conceptual difficulties (I do realise such question optimally shouldn't occur). The project aims to compare 8 RNA-seq samples (4 vs 4) testing for differentially expressed genes. The problem is that 2 of the samples (1 for each categories) weren’t ampl ...
rna-seq written 2.3 years ago by biostar.anon0 • updated 2.2 years ago by Biostar ♦♦ 20

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