User: ivar.grytten

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ivar.grytten20
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Posts by ivar.grytten

<prev • 6 results • page 1 of 1 • next >
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Answer: A: [MACS2] False negative peak calling problem
... When I have been debugging MACS2 peaks before, I have done something like this: - Check the output treatment bdg file that macs give when you specify --bdg. Locate the given area where you expect a peak - Check the backgrount bdg file for the same area - Check that the computed p-value using that s ...
written 9 weeks ago by ivar.grytten20
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Comment: C: Different position of the same alternative locus
... Thanks, that answers my question ...
written 16 months ago by ivar.grytten20
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Different position of the same alternative locus
... Where do people get the position of GRCh38 alternative loci? I've found multiple sources, and they seem to give different positions of some alternative loci. If I download the patch 9 dataset from http://www.ebi.ac.uk/ena/data/view/GCA_000001405.24 (by clicking "regions" in the top right corner), ...
genome grch38 alternative loci written 16 months ago by ivar.grytten20 • updated 16 months ago by deanna.church1.1k
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Answer: A: Is it possible to rerun an encode pipeline?
... After searching around a lot, I've concluded that Encode does not let you reproduce their pipelines without using dnanexus.com. However, I found this that works for the atac seq pipeline: https://github.com/kundajelab/atac_dnase_pipelines Quote from github repo: > The ATAC-seq pipeline specifi ...
written 16 months ago by ivar.grytten20
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Is it possible to rerun an encode pipeline?
... Assume I want to reproduce the results from an encode exeriment (e.g. this: https://www.encodeproject.org/experiments/ENCSR000EIY/), is that possible? I know it is possible using dnanexus.com service, but is this possible to do it without using dnanexus? It seems that the data from each experimen ...
encode alignment written 18 months ago by ivar.grytten20
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What are the flanking regions in alt loci of GRCh38?
... All alt loci of GRCh38 seem to have "flanking regions", long regions at the beginning and end of each alt loci, identical to the sequence at the "main path" (the non-alt part of the reference). I cannot seem to find any explanation anywhere on why these flanking regions are included in the alt loci ...
alt loci genome grch38 reference genome written 20 months ago by ivar.grytten20

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