User: ivar.grytten

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ivar.grytten40
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Posts by ivar.grytten

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Genome Browser Figure
... I know this answer comes late, but I came over this question myself just recently searching for tools to do what you want (so I guess other people might do the same). I've now tried a few tools, and from my experience these two work really well: - PyGenomeTracks: https://github.com/deeptools/pyGe ...
written 7 months ago by ivar.grytten40
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Answer: A: Evaluating alignment performance in vg
... I've also had struggles getting the map-sim script to work -- simlarly to you I was stuck at creating the sim-base and hap-base graphs. I figured it out in the end, and have made a simple tool here based on the map-sim script basically just requires an individual vcf file (e.g. the HG002 file that ...
written 8 months ago by ivar.grytten40
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Comment: C: Bwa Mem Have Different Alignment Result When Using Different Threads
... I can confirm that I am having this problem with bwa version 0.7.12. ...
written 22 months ago by ivar.grytten40
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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 2.3 years ago by ivar.grytten40
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Comment: C: Different position of the same alternative locus
... Thanks, that answers my question ...
written 3.5 years ago by ivar.grytten40
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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 3.5 years ago by ivar.grytten40 • updated 3.5 years 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 3.5 years ago by ivar.grytten40
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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 3.6 years ago by ivar.grytten40 • updated 10 months ago by Biostar ♦♦ 20
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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 3.8 years ago by ivar.grytten40

Latest awards to ivar.grytten

Popular Question 4 months ago, created a question with more than 1,000 views. For What are the flanking regions in alt loci of GRCh38?
Popular Question 6 months ago, created a question with more than 1,000 views. For Is it possible to rerun an encode pipeline?
Popular Question 6 months ago, created a question with more than 1,000 views. For Different position of the same alternative locus

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