User: hibernicah
hibernicah • 20
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Posts by hibernicah
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... At the end we used DESeq2 for Ribo-Seq and RNA-Seq separately as you suggested. Then we used change in translation efficiency (TE) log2(normalised expression measured by Ribo-Seq/normalised expression measured by RNA-Seq) to identify translationally regulated genes. We set arbitrary threshold for th ...
written 11 months ago by
hibernicah • 20
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... 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 ...
written 12 months ago by
hibernicah • 20
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... 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 12 months ago by
hibernicah • 20
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... 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 ...
written 14 months ago by
hibernicah • 20
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... 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 14 months ago by
hibernicah • 20
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... 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 14 months ago by
hibernicah • 20
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... 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 2.2 years ago by
hibernicah • 20
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... 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 2.2 years ago by
hibernicah • 20
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... 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 ...
written 2.2 years ago by
hibernicah • 20
• updated
9 weeks ago by
Saeed • 0
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