User: piyushjo

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piyushjo110
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Posts by piyushjo

<prev • 61 results • page 1 of 7 • next >
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Comment: C: what is inverse normalized RNA-seq expression and how to do that?
... Hi Kevin. Thanks for your response. I did see that particular thread and the cited paper. However, I didn't understand how to apply the suggested formula to RNA-expression. > qnorm((rank(x,na.last="keep")-0.5)/sum(!is.na(x))) For example, what is X? Gene expression value or gene name, and what ...
written 24 days ago by piyushjo110
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what is inverse normalized RNA-seq expression and how to do that?
... Hi, I just found out this new term "inverse normalized gene expression". I am reading a [paper][1] where they use inverse normalized expression instead of rpkm or vst normalized data for cox regression. Below is the statement from the publication. > It is common to find extreme outliers in larg ...
normalization rna-seq written 25 days ago by piyushjo110
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Answer: A: Get mRNA sequence from UCSC genome browser using coordinates
... Instead of UCSC browser you should try Ensembl Biomart. You can get mRNA sequence of each transcript of a gene. For few genes you can use their [browser][1], for larger gene list you can use [R library][2]. [1]: https://www.ensembl.org/biomart [2]: https://bioconductor.org/packages/release/bio ...
written 4 weeks ago by piyushjo110
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Answer: A: Differential Expression of lncRNAs in Brain --- Can a database aid my search?
... Hi JTA, Nice to see another person looking for lncRNA in brain. I can share some resources I am aware of. http://www.brainspan.org/ http://www.cdtdb.neuroinf.jp/CDT/Top.jsp Read these papers http://www.jneurosci.org/content/38/10/2399 https://genome.cshlp.org/content/28/8/1097.full https://w ...
written 7 weeks ago by piyushjo110
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Comment: C: Comparing stranded reads to unstranded reads
... Ok. Thanks. I am comparing cerebellum to medulloblastoma (cancer of cerebellum). The only thing I think bothers me is if the anti-sense transcripts for an overlapping mRNA would be improperly quantified. ...
written 8 weeks ago by piyushjo110
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Comment: C: Comparing stranded reads to unstranded reads
... But main question is just because one library is stranded and the other is unstranded, would that make them incomparable? I understand differences from human and machines are also involved. ...
written 8 weeks ago by piyushjo110
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Comment: C: Comparing stranded reads to unstranded reads
... But doesn't DESeq2 takes into account the difference in library depth? What else could be contributing to variation? ...
written 8 weeks ago by piyushjo110
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Comparing stranded reads to unstranded reads
... Hi, I have two datasets from different sources. Unfortunately one group have done unstranded RNA-seq while the second one has done stranded. When I do the PCA analysis of normalized reads using DESeq2, I see them clustering far from each other. Now I am doubtful if there is an artefact coming from ...
de gene strand information rna-seq written 8 weeks ago by piyushjo110 • updated 8 weeks ago by johnsonnathant80
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Comment: C: Tips for network prediction: WGCNA vs ARACNE (or MINET)
... Hi Fuyingxue, Thanks for your input and sharing the review article. ...
written 9 weeks ago by piyushjo110
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Comment: C: RNA-strandness of single cell library prep methods
... Sorry! I used the imagedb website. ...
written 11 weeks ago by piyushjo110

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