User: khorms
khorms • 210
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Posts by khorms
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... I don't think there is a standard protocol for this, try different lengths.
Regarding the background: if you do shuffling, make sure to keep the dinucleotide content (it's a very important predictor for many biological features). If you choose random positions from the genome, pick the ones where (1 ...
written 3 months ago by
khorms • 210
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... Oh nice, good to hear that! ...
written 3 months ago by
khorms • 210
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... I wonder what happened in the end? What did you choose? ...
written 3 months ago by
khorms • 210
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... I think there are plenty of tools that do this whole thing automatically for you; for example, see [CRIES][1]
[1]: https://github.com/csglab/CRIES ...
written 4 months ago by
khorms • 210
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... I see; of the top of my head, I don't know any gene enrichment analysis tools that take replicates into account. Maybe you could use something like StereoGene ([link][1]) directly on your peaks? Now, if you want to do the search on gene level: in our lab, we use our own tool called iPAGE because it ...
written 4 months ago by
khorms • 210
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... Can you elaborate on what are you trying to accomplish? Do you have a list of peaks thresholded (peak / not a peak), or do you have a list of peaks ranked with p-values with no threshold? What kinds of pathways are you looking for: regulons, GO pathways, genome-wide correlations, etc? ...
written 4 months ago by
khorms • 210
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... Yes there are definitely methods for DE comparisons implemented in the commonly used single cell packages; for example, see this discussion ([link][1]) for scanpy
[1]: https://github.com/theislab/scanpy/issues/397 ...
written 4 months ago by
khorms • 210
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... When you are looking for overrepresented k-mers in biological sequences, you are usually comparing one group of sequences to another. That means that the background distribution has to come from the control group of sequences. I am not sure how are you planning to incorporate such background distrib ...
written 4 months ago by
khorms • 210
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Comment:
C: FeatureCounts with scRNA-seq
... Can you add a link to this article? ...
written 4 months ago by
khorms • 210
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... Is there a standard format for SHAPE RNA reactivity data? I am struggling to find one
Looks like RNAstructure uses a two-column [format][1], ViennaRNA documentation doesn't talk about it too much [link][2]. It looks like every RNA lab does their own thing, is that so or am I missing something?
[ ...
written 4 months ago by
khorms • 210
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