User: Claire

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Claire40
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New User
Location:
Germany
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1 week, 3 days ago
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3 months, 1 week ago
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Posts by Claire

<prev • 28 results • page 1 of 3 • next >
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Strange distribution of logFC
... Dear all, I have RNAseq data of two groups. After doing differential gene expression using edgeR and DESeq2(the results are similar). I found the distribution of logFC is a little strange, having two peaks in the distribution. My guess would be that most genes are equally enriched in both goups, i ...
differential expressed genes rna-seq edger written 4 weeks ago by Claire40 • updated 4 weeks ago by Devon Ryan74k
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... I am not sure "RNA is composed of exons" is true after reading [this paper][1]. I don't want to be rude. I just want to know whether my understanding is right. [1]: https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-8-149 ...
written 9 weeks ago by Claire40
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... I don't agree with what you said about differntial isform/CDS usage. Differential isoform expression (DIE) and differential isoform usage (DIU) are related but distinct concepts. DIE assesses the difference of absolute expression in isoform level. In contrast, DIU assesses the difference of relative ...
written 9 weeks ago by Claire40
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... Sorry about the misunderstanding caused by my poor English, I am not meaning bad. What I mean when I say biology is too complex, is that when we analyze some biology problems, sometimes we have to do some compromise. For example, when we talk about measuring gene expression level, it is based on t ...
written 9 weeks ago by Claire40
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... The biology is too complex... I know that the eukaryotic genomes are pervasively transcribed, and that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and many biological processes utilize and require noncoding RNAs. But when we talk about ...
written 9 weeks ago by Claire40
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... Since in the annotation gtf file I see "exon" and "CDS". I thought edfferential expressed gene analysis could be based on CDS, which is more meaningful in my understanding ...
written 9 weeks ago by Claire40
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... Since in the annotation gtf file I see "exon" and "CDS". chr1 unknown exon 3214482 3216968 …... chr1 unknown stop_codon 3216022 3216024 …... chr1 unknown CDS 3216025 3216968 …... chr1 unknown CDS 3421702 3421901 …... ...
written 9 weeks ago by Claire40
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Differential gene expression based on "exon" or "CDS"?
... Hi all, When we talk about differential gene expression analysis using RNA-seq data, what we actually evaluate is the expression of "exon" or "CDS"? ![enter image description here][1] [1]: https://i.imgur.com/NJmVWeZ.png ...
gene rna-seq written 9 weeks ago by Claire40 • updated 9 weeks ago by Devon Ryan74k
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Comment: C: detailed explanation of Insert Size
... Thank you for your advice, I will give it a try. ...
written 9 weeks ago by Claire40
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Comment: C: detailed explanation of Insert Size
... Thank you for your clear explanation! ...
written 9 weeks ago by Claire40

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