Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds28k
Reputation:
28,220
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Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
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Google Scholar Page
Last seen:
8 hours ago
Joined:
9 years, 7 months ago
Email:
a************@gmail.com

One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.

Posts by Alex Reynolds

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Answer: A: Which non-parametric statistical test should I use for pairwise comparisons: Man
... You might use [distance correlation][1] to measure dependence. Distance metrics run from 0 (independence) to 1 (dependence). This should give a quantitative measurement that would bolster choice of testing. If pairs of samples between treatments appear to show dependence, then you might prefer [Wil ...
written 4 days ago by Alex Reynolds28k
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Answer: C: How to find which genes are transcriptional factors from a list of genes?
... JASPAR, TRANSFAC, UniPROBE, and Taipale are databases that include human TFs. You could also search GeneCards, I think, but I think you'd have to pay for their web service in order to automate searches on many TFs/genes. ...
written 11 days ago by Alex Reynolds28k
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Answer: A: Given a bed file with range of peaks, is it possible to identify the summit of t
... Maybe the DNase I hotspot calling algorithm here would be of use: https://github.com/Altius/hotspot2 Hotspot2 counts reads in a BAM file with a sliding window over the genome and identifies "hot" regions of interest, i.e. peaks of fixed or variable widths, with statistical scores that can be used ...
written 16 days ago by Alex Reynolds28k
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Answer: A: Increase height of box plots in ggplot
... The data are the data. You can't make box plots "higher" without changing the standard definition of a box plot, but you could change the data that go into calculating their features (IQR, etc.), so that box plots show you a relevant subset of your data. You could filter outliers to this subset usi ...
written 16 days ago by Alex Reynolds28k
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Comment: C: Picking random SNPs from 1000 Genomes using Vcftools
... My advice would be not to use this answer. ...
written 16 days ago by Alex Reynolds28k
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Answer: A: bedtools slop set start to -1
... Here's an alternative method: $ bedops --range 10000 --everything genes.bed > genes.pad10k.bed This assumes `genes.bed` is sorted per `sort-bed`. If not: $ bedops --range 10000 --everything <(sort-bed genes.bed) > genes.pad10k.bed No genome bounds are specified, but that can be ...
written 23 days ago by Alex Reynolds28k
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Comment: C: bedmap window base overlap not reporting what I would expect
... That makes sense. If your repeats overlap, i.e. are not disjoint, then you could potentially get multiple counts over a (50kb) window. Merging or partitioning your repeats would give you disjoint regions: $ bedops --merge repeats.bed > repeats.merged.bed $ bedops --partition repeats.bed ...
written 23 days ago by Alex Reynolds28k
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Answer: A: bedmap window base overlap not reporting what I would expect
... Use of `bedmap` requires `sort-bed`-sorted inputs in order to walk through files in correct order and to calculate correct statistics. If extracting a chromosome from your repeats works, then chromosomes in the original file are perhaps out of order. So I would suggest ensuring that `genome.all_re ...
written 25 days ago by Alex Reynolds28k
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Answer: A: How to tell if a BigWig file is 1-based or 0-based?
... I had asked UCSC a similar question some years ago, and their answer suggests to look at the header information, or to find the provenance of the data going into creation of the original bigWig: > The original data that is used to generate a bigWig can come from different formats. There is bedGr ...
written 25 days ago by Alex Reynolds28k
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Comment: C: Get genomic coordinates from gene names
... Gencode has mouse annotations. ...
written 28 days ago by Alex Reynolds28k

Latest awards to Alex Reynolds

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 4 days ago, created a post with more than 5 votes. For A: Find Nearest Gene Upstream Using Mysql And Perl Program
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 18 days ago, created a post with more than 5 votes. For A: Find Nearest Gene Upstream Using Mysql And Perl Program
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Any Method Of Converting Bigwig File Format Into Bed Format?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Any Method Of Converting Bigwig File Format Into Bed Format?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 3 months ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Appreciated 3 months ago, created a post with more than 5 votes. For Automating Gorilla And/Or Revigo Analysis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?

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