User: hibernicah

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hibernicah10
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Posts by hibernicah

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Pseudogenes masking during short-reads alignment
... Do you think that pseudogenes masking for short-reads mapping is sensible? I'm analysing ribosome profiling data that are about 25-32 nt long and even after standard pre-alignment to rRNA region I still see some multi mapping that maybe could be diminished if pseudogenes regions were hard-masked in ...
alignment rna-seq ribosomeprofiling written 4 days ago by hibernicah10
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Comment: C: Functional annotation of pathways in a genelist
... In order to narrow down a list of GO/pathways you can explore the pathways in terms of GO hierarchy as I mentioned earlier or simply adding more stringent threshold for significance, minimum or maximum number of genes in the pathway that was in an input list etc. ...
written 4 days ago by hibernicah10
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clusterProfiler GSEA for upregulated and downregulated gene sets: conflicting results
... I'm using `GSEA` function to perform enrichment analysis on my pre-ranked gene list. The function takes only genes sorted in decreasing order by a metric of choice, so I've ordered genes by decreasing DESeq2 test statistics, which reflects direction and significance of change. When I revert the or ...
deseq2 clusterprofiler gsea written 9 weeks ago by hibernicah10
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Comment: C: Functional annotation of pathways in a genelist
... What do you mean by further analysis? Do you see eg. stress response associated signatures enrichment and you want to summarise them for visualisation or do you want to draw more general conclusions from your data that you were unable to see so far? ...
written 9 weeks ago by hibernicah10
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Answer: A: Functional annotation of pathways in a genelist
... Gene ontologies are organised into a hierarchical tree structure, which means that smaller gene sets are usually a subset of a larger, broader set that may be helpful to categorise your results. You can also explore annotated relationship between them, see: [http://geneontology.org/docs/ontology-rel ...
written 9 weeks ago by hibernicah10
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Comment: C: Ribo-Seq multi time course analysis with DESeq2
... Yes I agree. The problem is that translation changes are highly correlated with transcript abundance and we don't know what is the "normal" translational response to changing mRNA abundance. The safe option seems to be define translationally regulated genes as genes that shows changes only in the Ri ...
written 14 months ago by hibernicah10
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Comment: C: Ribo-Seq multi time course analysis with DESeq2
... Thank you for such a quick reply. This is a good point. Usually with a simple experiment design I do separate analyses for RNA-Seq and Ribo-Seq experiment, which in that case should look like this: dds <- DESeqDataSetFromMatrix(counts, ~ cell_line + condition + time + condition:time) dds ...
written 14 months ago by hibernicah10
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Ribo-Seq multi time course analysis with DESeq2
... I am analysing the following experiment: two cell lines representing the same disease subtype were treated with a drug or DMSO (control) and the samples were collected in 4 time points: 0.5, 1, 6, and 16 h. Two types of sequencing were performed for each sample: Ribo-Seq to measure translatome and R ...
ribo-seq deseq2 design sequencing written 14 months ago by hibernicah10

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