Moderator: Alex Reynolds
Alex Reynolds ♦ 28k
- Reputation:
- 28,220
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- Location:
- Seattle, WA USA
- Website:
- http://bitsumma.com/
- Twitter:
- AlexReynolds
- Scholar ID:
- 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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... 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 Reynolds ♦ 28k
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... 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 Reynolds ♦ 28k
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... 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 Reynolds ♦ 28k
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... 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 Reynolds ♦ 28k
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... My advice would be not to use this answer. ...
written 16 days ago by
Alex Reynolds ♦ 28k
2
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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 Reynolds ♦ 28k
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... 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 Reynolds ♦ 28k
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... 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 Reynolds ♦ 28k
2
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... 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 Reynolds ♦ 28k
0
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2
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159
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... Gencode has mouse annotations. ...
written 28 days ago by
Alex Reynolds ♦ 28k
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For A: Do these warning messages during my bedops install mean bedops won't work proper
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For A: Find Nearest Gene Upstream Using Mysql And Perl Program
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