Moderator: Alex Reynolds

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Alex Reynolds19k
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Seattle, WA USA
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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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Comment: C: tabix for ID column
... Don't overthink it. [Link `gzip` and `gunzip` to `pigz`][1]. Then: $ gzip -c snps.vcf > snps.gz $ zgrep rs1234 snps.gz > answer.txt A database is way overkill. [1]: https://unix.stackexchange.com/a/87120/38132 ...
written 1 day ago by Alex Reynolds19k
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Comment: C: Find genes neighboring to gene of interest
... There are [lots of answers][1] on this question already on Biostars. Search for "[closest-features][2]" and look at the `--closest` and `--dist` options. [1]: https://www.biostars.org/p/53587/ [2]: http://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html ...
written 8 days ago by Alex Reynolds19k
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Answer: A: get intervals of a fraction of bed-files
... Here is an efficient solution with [BEDOPS][1], which avoids approaches with other tools that require M^N pairwise comparisons, for M elements and N sets. Say you have N files (your specific example uses 8 files, but this shows a generic solution for N files). You want all elements from N files, wh ...
written 11 days ago by Alex Reynolds19k
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Comment: C: How To Sort Bed Format File
... Yep, see: https://www.biostars.org/p/64687/#64701 ...
written 11 days ago by Alex Reynolds19k
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Answer: A: how to randomly select intervals of different lengths (not records) from a BED f
... It looks like a pretty straightforward scripting problem. You could efficiently solve overlaps at the end with `bedops --partition`, which is not available in other toolkits, as far as I know. Here's a script you can use to subsample from a shuffled list of intervals: #!/usr/bin/env python ...
written 13 days ago by Alex Reynolds19k
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Comment: C: Filter for regions containing large stretches of missing data
... I'm just explaining one way to do things, if your inputs can be set up correctly. You may need to convert files to sorted BED with `bigWigToWig`, `wig2bed`, `jq`, `sort-bed` etc. to do set operations. ...
written 15 days ago by Alex Reynolds19k
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Answer: A: Filter for regions containing large stretches of missing data
... Merge the per-base signal (scores): $ bedops --merge per-base-signal.bed > merged-pbs.bed Invert the merged regions to get the "mirror" image. This "mirror" is the set of gaps in between merged stretches of signal. Assuming `hg38`, say: $ fetchChromSizes hg38 | awk '{ print $1"\t0\t" ...
written 15 days ago by Alex Reynolds19k
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Comment: C: Quickly Plotting Distribution Of Points From Bed File?
... Another option is to use `bedops --chop` to make the 10k windows, instead of `awk`: $ bedops --chop 10000 mm10.extents.bed > mm10.disjointWindows.bed This option was added after I wrote the initial answer. ...
written 17 days ago by Alex Reynolds19k
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Comment: C: Quickly Plotting Distribution Of Points From Bed File?
... Ah, sorry, I misread. I'm not sure why you get an empty result. I'd break things down and use `head` to see what comes out at various stages. ...
written 17 days ago by Alex Reynolds19k
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Comment: C: Quickly Plotting Distribution Of Points From Bed File?
... Yeah, not sure why that is. Maybe do: $ fetchChromSizes mm10 | head and see what you get. ...
written 17 days ago by Alex Reynolds19k

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Teacher 8 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 10 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?
Scholar 12 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 15 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: How To Randomly Sample A Subset Of Lines From A Bed File
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Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Randomly Sample A Subset Of Lines From A Bed File
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Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How To Randomly Sample A Subset Of Lines From A Bed File
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Scholar 5 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 7 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper

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